Thanks for showing me the right direction.
Actually I was using Jsreport 4.6.0 in first place and it was working in dev mode of electron (where the chromium downloaded by puppeteer was in User/.cache/puppeteer folder and version 4.6.0 already had a fix for this problem of permissions.)
Once I packaged the app, chrome-pdf shown said issue as I had copied the chromium files inside my application package directory (which did not have the permissions). using icacls on this specific directory path did fix the issue however this seems difficult to setup once I package my app and distribute where I probably wont have the permissions to run icacls.
It seems like the fix available in 4.6.0 is only applying to default path of puppeteer.
Is there any way to apply the fix to the chromium path specified in launchOptions of jsreport.config.json