diff --git a/main/src/main/scala/sbt/Defaults.scala b/main/src/main/scala/sbt/Defaults.scala
index bbb27c9e0..c4f7468b5 100644
--- a/main/src/main/scala/sbt/Defaults.scala
+++ b/main/src/main/scala/sbt/Defaults.scala
@@ -2030,7 +2030,10 @@ object Defaults extends BuildCommon {
               val xapisFiles = xapis.map { (k, v) =>
                 converter.toPath(k).toFile() -> v
               }
-              val options = sOpts ++ Opts.doc.externalAPI(xapisFiles)
+              val externalApiOpts =
+                if (ScalaArtifacts.isScala3(sv)) Opts.doc.externalAPIScala3(xapisFiles)
+                else Opts.doc.externalAPI(xapisFiles)
+              val options = sOpts ++ externalApiOpts
               val scalac = cs.scalac match
                 case ac: AnalyzingCompiler => ac.onArgs(exported(s, "scaladoc"))
               val docSrcFiles = if ScalaArtifacts.isScala3(sv) then tFiles else srcs
diff --git a/main/src/main/scala/sbt/Opts.scala b/main/src/main/scala/sbt/Opts.scala
index 10c7417d6..faa54abfa 100644
--- a/main/src/main/scala/sbt/Opts.scala
+++ b/main/src/main/scala/sbt/Opts.scala
@@ -38,6 +38,37 @@ object Opts {
         mappings
           .map { (f, u) => s"${f.getAbsolutePath}#${u.toURL().toExternalForm}" }
           .mkString("-doc-external-doc:", ",", "") :: Nil
+
+    /**
+     * Generates Scala 3 scaladoc external mappings option.
+     * Format: -external-mappings:regex::[scaladoc3|scaladoc|javadoc]::url,...
+     */
+    def externalAPIScala3(mappings: Iterable[(File, URI)]): Seq[String] =
+      if (mappings.isEmpty) Nil
+      else
+        mappings
+          .map { (f, u) =>
+            val fileName = f.getName
+            // Escape regex special characters in the filename
+            val escapedName = fileName.replaceAll("([\\[\\]{}()*+?.\\\\^$|])", "\\\\$1")
+            // Use a regex pattern that matches the file anywhere in the classpath
+            val regex = s".*$escapedName"
+            // Determine if this is javadoc or scaladoc based on the file/URL
+            val docType = if (isJavaDoc(f, u)) "javadoc" else "scaladoc3"
+            s"$regex::$docType::${u.toURL().toExternalForm}"
+          }
+          .mkString("-external-mappings:", ",", "") :: Nil
+
+    private def isJavaDoc(file: File, uri: URI): Boolean = {
+      val name = file.getName.toLowerCase
+      val url = uri.toString.toLowerCase
+      // Heuristics to detect Java documentation
+      name.startsWith("rt.jar") ||
+      name.contains("java") && !name.contains("scala") ||
+      url.contains("docs.oracle.com") ||
+      url.contains("javadoc") ||
+      url.contains("/java/") && !url.contains("scala")
+    }
   }
   object resolver {
     import sbt.io.syntax.*
diff --git a/sbt-app/src/sbt-test/actions/doc-external-scala3/build.sbt b/sbt-app/src/sbt-test/actions/doc-external-scala3/build.sbt
new file mode 100644
index 000000000..08af6cb8c
--- /dev/null
+++ b/sbt-app/src/sbt-test/actions/doc-external-scala3/build.sbt
@@ -0,0 +1,22 @@
+// Test for issue #6652: Doc task fails with `bad option '-doc-external-doc'` for scala3 project
+// This test verifies that autoAPIMappings works correctly with Scala 3's -external-mappings option
+
+lazy val root = (project in file("."))
+  .settings(
+    scalaVersion := "3.3.4",
+    autoAPIMappings := true,
+    libraryDependencies += "org.typelevel" %% "cats-core" % "2.12.0",
+    TaskKey[Unit]("checkDocGenerated") := {
+      val docDir = (Compile / doc / target).value
+      val indexFile = docDir / "index.html"
+      assert(indexFile.exists(), s"Expected $indexFile to exist after doc generation")
+      println(s"Documentation generated successfully at $docDir")
+    },
+    TaskKey[Unit]("checkApiMappings") := {
+      val mappings = (Compile / doc / apiMappings).value
+      println(s"API Mappings count: ${mappings.size}")
+      // With autoAPIMappings and cats-core dependency, we should have some mappings
+      // (cats-core publishes with apiURL)
+      println(s"API Mappings: ${mappings.take(3).mkString("\n  ", "\n  ", "")}")
+    }
+  )
diff --git a/sbt-app/src/sbt-test/actions/doc-external-scala3/src/main/scala/Example.scala b/sbt-app/src/sbt-test/actions/doc-external-scala3/src/main/scala/Example.scala
new file mode 100644
index 000000000..8ca12b898
--- /dev/null
+++ b/sbt-app/src/sbt-test/actions/doc-external-scala3/src/main/scala/Example.scala
@@ -0,0 +1,7 @@
+package example
+
+/** An example class to generate documentation for. */
+class Example {
+  /** Returns a greeting */
+  def greet: String = "Hello"
+}
diff --git a/sbt-app/src/sbt-test/actions/doc-external-scala3/test b/sbt-app/src/sbt-test/actions/doc-external-scala3/test
new file mode 100644
index 000000000..81fab5d94
--- /dev/null
+++ b/sbt-app/src/sbt-test/actions/doc-external-scala3/test
@@ -0,0 +1,12 @@
+# Test for issue #6652: Doc task should use -external-mappings for Scala 3
+# instead of -doc-external-doc which causes "bad option" warnings
+
+# Show the API mappings that will be used
+> checkApiMappings
+
+# Run the doc task - this should succeed without "bad option" warnings
+# Before the fix, this would emit a warning about bad option -doc-external-doc
+> doc
+
+# Verify documentation was actually generated
+> checkDocGenerated