Unable to login using secure cookie

In a vulnerability scan of our site, I got 2 vulnerabilities.

150122 Cookie Does Not Contain The "secure" Attribute
150123 Cookie Does Not Contain The "HTTPOnly" Attribute

I tried the following solutions.

Adding
session.cookie_httponly = True
session.cookie_secure = True

To the php.ini file
and
Header always edit Set-Cookie (.*) "$1; HTTPOnly"
Header always edit Set-Cookie (.*) "$1; Secure"

To the .htaccess file.
But when doing so, I am not able to login to the site.
Any suggestions on how to fix this?