fortinac keeps logging in to fortigate every few minutes generating too many alerts

FortiNAC periodically logs in to all network equipment, like to poll L2/L3 devices and so.

But where do you see the alerts? You mean on a separate monitoring solution? If this is the case then all monitoring solutions have a way to disable a specific alert. That's where you should disable them.

How is the FGT integrated with FNAC, does it have FSW, FAP or VPN integration configured?

Most of the communication now are done through API (page 67), L3 polling may still use SSH access to get the ARP table. You can also configure the REST API Administrator key as shown in page 10.