diff --git a/plugins/package-managers/pub/src/main/kotlin/utils/PubCacheReader.kt b/plugins/package-managers/pub/src/main/kotlin/utils/PubCacheReader.kt
index 2123f0e1d1c7..af5ec9460ec0 100644
--- a/plugins/package-managers/pub/src/main/kotlin/utils/PubCacheReader.kt
+++ b/plugins/package-managers/pub/src/main/kotlin/utils/PubCacheReader.kt
@@ -85,13 +85,13 @@ internal class PubCacheReader(flutterHome: File? = null) {
         val path = if (type == "hosted" && url.isNotEmpty()) {
             // Packages with source set to "hosted" and "url" key in description set to "https://pub.dartlang.org".
             // The path should be resolved to "hosted/pub.dartlang.org/packageName-packageVersion".
-            "hosted/${url.replace("https://", "")}/$packageName-$packageVersion"
+            "hosted/${url.replace("https://", "").replace("/", "%47")}/$packageName-$packageVersion"
         } else if (type == "git" && resolvedRef.isNotEmpty()) {
             // Packages with source set to "git" and a "resolved-ref" key in description set to a gitHash.
             // These packages do not define a packageName in the packageInfo, but by definition the path resolves to
             // the project name as given from the VcsHost and to the resolvedRef.
             val projectName = VcsHost.getProject(url) ?: return null
-            if (resolvedPath.isNotEmpty()) {
+            if (resolvedPath.isNotEmpty() && resolvedPath != ".") {
                 "git/$projectName-$resolvedRef/$resolvedPath"
             } else {
                 "git/$projectName-$resolvedRef"
diff --git a/plugins/package-managers/pub/src/test/kotlin/utils/PubCacheReaderTest.kt b/plugins/package-managers/pub/src/test/kotlin/utils/PubCacheReaderTest.kt
index c751589ec21c..58ffe23bd903 100644
--- a/plugins/package-managers/pub/src/test/kotlin/utils/PubCacheReaderTest.kt
+++ b/plugins/package-managers/pub/src/test/kotlin/utils/PubCacheReaderTest.kt
@@ -40,6 +40,9 @@ class PubCacheReaderTest : WordSpec({
     val gitPackageCacheDir = tmpPubCacheDir.resolve("git/$PACKAGE_NAME-$RESOLVED_REF")
     val gitPackageWithPathCacheDir = tmpPubCacheDir.resolve("git/$PACKAGE_NAME-$RESOLVED_REF/$PACKAGE_NAME")
     val hostedPackageCacheDir = tmpPubCacheDir.resolve("hosted/oss-review-toolkit.org/$PACKAGE_NAME-$PACKAGE_VERSION")
+    val customPackageCacheDir = tmpPubCacheDir.resolve(
+        "hosted/oss-review-toolkit.org%47api%47pub%47repository%47/$PACKAGE_NAME-$PACKAGE_VERSION"
+    )
     val localPackagePathAbsolute = ABSOLUTE_PATH
     val localPackagePathRelative = ABSOLUTE_PATH.resolve(RELATIVE_PATH)
 
@@ -49,6 +52,7 @@ class PubCacheReaderTest : WordSpec({
         gitPackageCacheDir.safeMkdirs()
         gitPackageWithPathCacheDir.safeMkdirs()
         hostedPackageCacheDir.safeMkdirs()
+        customPackageCacheDir.safeMkdirs()
     }
 
     "findProjectRoot" should {
@@ -72,6 +76,27 @@ class PubCacheReaderTest : WordSpec({
             ) shouldBe gitPackageCacheDir
         }
 
+        "resolve the path of a Git dependency with special path" {
+            reader.findProjectRoot(
+                jsonMapper.readTree(
+                    """
+                        {
+                            "dependency": "direct main",
+                            "description": {
+                                "path": ".",
+                                "ref": "master",
+                                "resolved-ref": "$RESOLVED_REF",
+                                "url": "https://github.com/oss-review-toolkit/$PACKAGE_NAME.git"
+                            },
+                            "source": "git",
+                            "version": "9.9.9"
+                        }
+                    """.trimIndent()
+                ),
+                ABSOLUTE_PATH // not used
+            ) shouldBe gitPackageCacheDir
+        }
+
         "resolve the path of a Git dependency with path" {
             reader.findProjectRoot(
                 jsonMapper.readTree(
@@ -112,6 +137,25 @@ class PubCacheReaderTest : WordSpec({
             ) shouldBe hostedPackageCacheDir
         }
 
+        "resolve the path of a custom package repository dependency" {
+            PubCacheReader().findProjectRoot(
+                jsonMapper.readTree(
+                    """
+                        {
+                            "dependency": "transitive",
+                            "description": {
+                                "name": "$PACKAGE_NAME",
+                                "url": "https://oss-review-toolkit.org/api/pub/repository/"
+                            },
+                            "source": "hosted",
+                            "version": "$PACKAGE_VERSION"
+                        }
+                    """.trimIndent()
+                ),
+                ABSOLUTE_PATH // not used
+            ) shouldBe customPackageCacheDir
+        }
+
         "resolve the relative path of a local dependency" {
             PubCacheReader().findProjectRoot(
                 jsonMapper.readTree(