diff --git a/compiler/fir/java/src/org/jetbrains/kotlin/fir/java/enhancement/EnhancedTypeForWarningAttribute.kt b/compiler/fir/java/src/org/jetbrains/kotlin/fir/java/enhancement/EnhancedTypeForWarningAttribute.kt
index 0edcf4a51bd..20d6844ae72 100644
--- a/compiler/fir/java/src/org/jetbrains/kotlin/fir/java/enhancement/EnhancedTypeForWarningAttribute.kt
+++ b/compiler/fir/java/src/org/jetbrains/kotlin/fir/java/enhancement/EnhancedTypeForWarningAttribute.kt
@@ -8,6 +8,7 @@ package org.jetbrains.kotlin.fir.java.enhancement
 import org.jetbrains.kotlin.builtins.jvm.JavaToKotlinClassMap
 import org.jetbrains.kotlin.fir.resolve.substitution.AbstractConeSubstitutor
 import org.jetbrains.kotlin.fir.types.*
+import org.jetbrains.kotlin.name.StandardClassIds
 import kotlin.reflect.KClass
 
 data class EnhancedTypeForWarningAttribute(
@@ -45,8 +46,10 @@ val ConeKotlinType.isEnhancedTypeForWarningDeprecation: Boolean
 class EnhancedForWarningConeSubstitutor(typeContext: ConeTypeContext) : AbstractConeSubstitutor(typeContext) {
     override fun substituteType(type: ConeKotlinType): ConeKotlinType? {
         // The attribute is usually taken from the lower bound of flexible types.
-        // However, if the type has flexible mutability, we don't want to accidentally enhance the mutability to the lower bound.
-        if (type is ConeFlexibleType && type.hasFlexibleMutability()) {
+        // However, if the type has flexible mutability or type argument variance,
+        // we can't just use the lower bound, otherwise we can get false positive mismatches
+        // because of the mutability or the type argument variance.
+        if (type is ConeFlexibleType && (type.hasFlexibleMutability() || type.isArrayWithFlexibleVariance())) {
             val lowerSubstituted = substituteOrNull(type.lowerBound)
 
             return if (lowerSubstituted is ConeSimpleKotlinType) {
@@ -67,7 +70,17 @@ class EnhancedForWarningConeSubstitutor(typeContext: ConeTypeContext) : Abstract
         return enhancedTopLevel?.let(::substituteOrSelf)
     }
 
+    /**
+     * `List<Object>` is represented as `MutableList<Any!>..List<Any!>?`.
+     */
     private fun ConeFlexibleType.hasFlexibleMutability(): Boolean {
         return JavaToKotlinClassMap.isMutable(lowerBound.classId) && JavaToKotlinClassMap.isReadOnly(upperBound.classId)
     }
+
+    /**
+     * `Object[]` is represented as `Array<Any>..Array<out Any>?`.
+     */
+    private fun ConeFlexibleType.isArrayWithFlexibleVariance(): Boolean {
+        return lowerBound.classId == StandardClassIds.Array && lowerBound.typeArguments.firstOrNull()?.kind != upperBound.typeArguments.firstOrNull()?.kind
+    }
 }
\ No newline at end of file
diff --git a/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.fir.kt b/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.fir.kt
index 2f5176ba3c4..045c922020a 100644
--- a/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.fir.kt
+++ b/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.fir.kt
@@ -18,6 +18,8 @@ public class BaseClass {
 
     public Foo explicitlyNullnessUnspecified(@NullnessUnspecified Foo x) { return null; }
 
+    public void withVararg(Object... p) { }
+
     public static Foo foo() { return null; }
 }
 
@@ -54,6 +56,8 @@ class Correct : IntermediateClass() {
     override fun intermediateNotNull(): Foo {
         return FOO
     }
+
+    override fun withVararg(vararg p: Any) {}
 }
 
 class WrongReturnTypes : IntermediateClass() {
diff --git a/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.kt b/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.kt
index 763b600bd71..30147b6cad6 100644
--- a/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.kt
+++ b/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.kt
@@ -18,6 +18,8 @@ public class BaseClass {
 
     public Foo explicitlyNullnessUnspecified(@NullnessUnspecified Foo x) { return null; }
 
+    public void withVararg(Object... p) { }
+
     public static Foo foo() { return null; }
 }
 
@@ -54,6 +56,8 @@ class Correct : IntermediateClass() {
     override fun intermediateNotNull(): Foo {
         return FOO
     }
+
+    override fun withVararg(vararg p: Any) {}
 }
 
 class WrongReturnTypes : IntermediateClass() {
diff --git a/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.txt b/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.txt
index ea98baa1665..847a602f14e 100644
--- a/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.txt
+++ b/compiler/testData/diagnostics/foreignAnnotationsTests/java8Tests/jspecify/warnMode/OverrideOfAnnotated.txt
@@ -12,6 +12,7 @@ private val FOO: FOO.`<no name provided>`
     public open override /*1*/ /*fake_override*/ fun hashCode(): kotlin.Int
     @org.jspecify.annotations.Nullable public open fun mixed(/*0*/ x: Foo!): @org.jspecify.annotations.Nullable Foo!
     public open override /*1*/ /*fake_override*/ fun toString(): kotlin.String
+    public open fun withVararg(/*0*/ vararg p: kotlin.Any! /*kotlin.Array<(out) kotlin.Any!>!*/): kotlin.Unit
 
     // Static members
     public open fun foo(): Foo!
@@ -28,6 +29,7 @@ public final class Correct : IntermediateClass {
     public open override /*1*/ fun intermediateNotNull(): Foo
     public open override /*1*/ fun mixed(/*0*/ x: Foo): Foo?
     public open override /*1*/ /*fake_override*/ fun toString(): kotlin.String
+    public open override /*1*/ fun withVararg(/*0*/ vararg p: kotlin.Any /*kotlin.Array<out kotlin.Any>*/): kotlin.Unit
 }
 
 public interface Foo {
@@ -47,6 +49,7 @@ public open class IntermediateClass : BaseClass {
     public open fun intermediateNotNull(): Foo!
     @org.jspecify.annotations.Nullable public open override /*1*/ /*fake_override*/ fun mixed(/*0*/ x: Foo!): @org.jspecify.annotations.Nullable Foo!
     public open override /*1*/ /*fake_override*/ fun toString(): kotlin.String
+    public open override /*1*/ /*fake_override*/ fun withVararg(/*0*/ vararg p: kotlin.Any! /*kotlin.Array<(out) kotlin.Any!>!*/): kotlin.Unit
 }
 
 public final class WrongParameter : IntermediateClass {
@@ -60,6 +63,7 @@ public final class WrongParameter : IntermediateClass {
     public open override /*1*/ /*fake_override*/ fun intermediateNotNull(): Foo!
     public open override /*1*/ fun mixed(/*0*/ x: Foo?): Foo?
     public open override /*1*/ /*fake_override*/ fun toString(): kotlin.String
+    public open override /*1*/ /*fake_override*/ fun withVararg(/*0*/ vararg p: kotlin.Any! /*kotlin.Array<(out) kotlin.Any!>!*/): kotlin.Unit
 }
 
 public final class WrongReturnTypes : IntermediateClass {
@@ -73,5 +77,6 @@ public final class WrongReturnTypes : IntermediateClass {
     public open override /*1*/ fun intermediateNotNull(): Foo?
     @org.jspecify.annotations.Nullable public open override /*1*/ /*fake_override*/ fun mixed(/*0*/ x: Foo!): @org.jspecify.annotations.Nullable Foo!
     public open override /*1*/ /*fake_override*/ fun toString(): kotlin.String
+    public open override /*1*/ /*fake_override*/ fun withVararg(/*0*/ vararg p: kotlin.Any! /*kotlin.Array<(out) kotlin.Any!>!*/): kotlin.Unit
 }