diff --git a/compiler/ballerina-lang/src/main/java/io/ballerina/projects/Project.java b/compiler/ballerina-lang/src/main/java/io/ballerina/projects/Project.java
index 7828865e2a93..c539eb65b357 100644
--- a/compiler/ballerina-lang/src/main/java/io/ballerina/projects/Project.java
+++ b/compiler/ballerina-lang/src/main/java/io/ballerina/projects/Project.java
@@ -18,7 +18,6 @@
 package io.ballerina.projects;
 
 import io.ballerina.projects.environment.ProjectEnvironment;
-import org.wso2.ballerinalang.compiler.PackageCache;
 import org.wso2.ballerinalang.compiler.util.CompilerContext;
 import org.wso2.ballerinalang.compiler.util.CompilerOptions;
 
@@ -36,7 +35,7 @@ public abstract class Project {
     protected final Path sourceRoot;
     private Package currentPackage;
     private BuildOptions buildOptions;
-    private final ProjectEnvironment projectEnvironment;
+    protected ProjectEnvironment projectEnvironment;
     private final ProjectKind projectKind;
 
     protected Project(ProjectKind projectKind,
@@ -110,13 +109,7 @@ protected void populateCompilerContext() {
      * (i.e. package resolution caches, compilation caches)
      * generated during project compilation will be discarded.
      */
-    public void clearCaches() {
-        cloneProject(this);
-        CompilerContext compilerContext = this.projectEnvironmentContext()
-                .getService(CompilerContext.class);
-        PackageCache packageCache = PackageCache.getInstance(compilerContext);
-        packageCache.flush();
-    }
+    public abstract void clearCaches();
 
     /**
      * Creates a new Project instance which has the same structure as this Project.
@@ -128,7 +121,7 @@ public void clearCaches() {
      */
     public abstract Project duplicate();
 
-    protected Project cloneProject(Project project) {
+    protected Project resetPackage(Project project) {
         Package clone = this.currentPackage.duplicate(project);
         project.setCurrentPackage(clone);
         return project;
diff --git a/compiler/ballerina-lang/src/main/java/io/ballerina/projects/bala/BalaProject.java b/compiler/ballerina-lang/src/main/java/io/ballerina/projects/bala/BalaProject.java
index 199077eceea9..81febf8d9c61 100644
--- a/compiler/ballerina-lang/src/main/java/io/ballerina/projects/bala/BalaProject.java
+++ b/compiler/ballerina-lang/src/main/java/io/ballerina/projects/bala/BalaProject.java
@@ -63,12 +63,20 @@ private BalaProject(ProjectEnvironmentBuilder environmentBuilder, Path balaPath)
         this.platform = BalaFiles.readPackageJson(balaPath).getPlatform();
     }
 
+    @Override
+    public void clearCaches() {
+        resetPackage(this);
+        ProjectEnvironmentBuilder projectEnvironmentBuilder = ProjectEnvironmentBuilder.getDefaultBuilder();
+        projectEnvironmentBuilder.addCompilationCacheFactory(TempDirCompilationCache::from);
+        this.projectEnvironment = projectEnvironmentBuilder.build(this);
+    }
+
     @Override
     public Project duplicate() {
         ProjectEnvironmentBuilder projectEnvironmentBuilder = ProjectEnvironmentBuilder.getDefaultBuilder();
         projectEnvironmentBuilder.addCompilationCacheFactory(TempDirCompilationCache::from);
         BalaProject balaProject = new BalaProject(projectEnvironmentBuilder, this.sourceRoot);
-        return cloneProject(balaProject);
+        return resetPackage(balaProject);
     }
 
     @Override
diff --git a/compiler/ballerina-lang/src/main/java/io/ballerina/projects/directory/BuildProject.java b/compiler/ballerina-lang/src/main/java/io/ballerina/projects/directory/BuildProject.java
index a1cc2edd072e..f5812bc1e4ff 100644
--- a/compiler/ballerina-lang/src/main/java/io/ballerina/projects/directory/BuildProject.java
+++ b/compiler/ballerina-lang/src/main/java/io/ballerina/projects/directory/BuildProject.java
@@ -155,12 +155,18 @@ public Optional<Path> documentPath(DocumentId documentId) {
         return Optional.empty();
     }
 
+    @Override
+    public void clearCaches() {
+        resetPackage(this);
+        this.projectEnvironment = ProjectEnvironmentBuilder.getDefaultBuilder().build(this);
+    }
+
     @Override
     public Project duplicate() {
         BuildOptions duplicateBuildOptions = BuildOptions.builder().build().acceptTheirs(buildOptions());
         BuildProject buildProject = new BuildProject(
                 ProjectEnvironmentBuilder.getDefaultBuilder(), this.sourceRoot, duplicateBuildOptions);
-        return cloneProject(buildProject);
+        return resetPackage(buildProject);
     }
 
     @Override
diff --git a/compiler/ballerina-lang/src/main/java/io/ballerina/projects/directory/SingleFileProject.java b/compiler/ballerina-lang/src/main/java/io/ballerina/projects/directory/SingleFileProject.java
index 49338b77b497..d84efcb85430 100644
--- a/compiler/ballerina-lang/src/main/java/io/ballerina/projects/directory/SingleFileProject.java
+++ b/compiler/ballerina-lang/src/main/java/io/ballerina/projects/directory/SingleFileProject.java
@@ -25,6 +25,7 @@
 import io.ballerina.projects.ProjectException;
 import io.ballerina.projects.ProjectKind;
 import io.ballerina.projects.internal.PackageConfigCreator;
+import io.ballerina.projects.repos.TempDirCompilationCache;
 
 import java.io.IOException;
 import java.nio.file.Files;
@@ -82,12 +83,20 @@ private SingleFileProject(ProjectEnvironmentBuilder environmentBuilder, Path fil
         populateCompilerContext();
     }
 
+    @Override
+    public void clearCaches() {
+        resetPackage(this);
+        ProjectEnvironmentBuilder projectEnvironmentBuilder = ProjectEnvironmentBuilder.getDefaultBuilder();
+        projectEnvironmentBuilder.addCompilationCacheFactory(TempDirCompilationCache::from);
+        this.projectEnvironment = projectEnvironmentBuilder.build(this);
+    }
+
     @Override
     public Project duplicate() {
         BuildOptions duplicateBuildOptions = BuildOptions.builder().build().acceptTheirs(buildOptions());
         SingleFileProject singleFileProject = new SingleFileProject(
                 ProjectEnvironmentBuilder.getDefaultBuilder(), this.sourceRoot, duplicateBuildOptions);
-        return cloneProject(singleFileProject);
+        return resetPackage(singleFileProject);
     }
 
     @Override