diff --git a/java/ql/src/utils/model-generator/GenerateFlowModel.py b/java/ql/src/utils/model-generator/GenerateFlowModel.py
index 559c9444017..44b40a4d34a 100755
--- a/java/ql/src/utils/model-generator/GenerateFlowModel.py
+++ b/java/ql/src/utils/model-generator/GenerateFlowModel.py
@@ -1,5 +1,14 @@
 #!/usr/bin/python3
 
+import sys
+import os.path
+import subprocess
+
+# Add Model as Data script directory to sys.path.
+gitroot = subprocess.check_output(["git", "rev-parse", "--show-toplevel"]).decode("utf-8").strip()
+madpath = os.path.join(gitroot, "misc/scripts/models-as-data/")
+sys.path.append(madpath)
+
 import generate_flow_model as model
 
 language = "java"
diff --git a/misc/scripts/models-as-data/generate_flow_model.py b/misc/scripts/models-as-data/generate_flow_model.py
index 1960be7b259..2c124b30b67 100644
--- a/misc/scripts/models-as-data/generate_flow_model.py
+++ b/misc/scripts/models-as-data/generate_flow_model.py
@@ -93,8 +93,7 @@ Requirements: `codeql` should both appear on your path.
 
     def runQuery(self, infoMessage, query):
         print("########## Querying " + infoMessage + "...")
-        queryFile = os.path.join(os.path.dirname(
-            __file__), query)
+        queryFile = os.path.join(self.codeQlRoot, f"{self.language}/ql/src/utils/model-generator", query)
         resultBqrs = os.path.join(self.workDir, "out.bqrs")
         cmd = ['codeql', 'query', 'run', queryFile, '--database',
                self.database, '--output', resultBqrs, '--threads', '8']