Cookie set on client side(javascript) marked it as httpOnly. I searched all JS files used in my website if anywhere we are using HttpOnly but did not find it. Something else is causing this flag set to true by default. What could the issue? I may not be able to post all thousands of lines of code here..
If while setting the cookie it is marked as secure by the server it is httponly, ie not accessible via client side javascripts (either your or others).
Look for the place where cookie is being set by the backend code and do not mark it as secure if that is what you want.