A tricolour and another nationalist flag appeared on flag poles over Parliament Buildings earlier in June.
DUP MLA Paula Bradley, who sits on the assembly commission, had expressed concern about a claim from a republican group called the 1916 societies.
It indicated they had hoisted the flags over Stormont.
At the assembly on Tuesday, Mrs Bradley asked if the police had made any assessment of the risk within Parliament Buildings.
She asked what "steps have been taken to ensure the safety of the building has not been compromised?"
In response, a PSNI officer writing on behalf of Ch Con George Hamilton said the police were limited in what they could say as a full investigation of the flag incident is currently under way.
However, the PSNI added that "it would be the recommendation of police that a full review of internal security be undertaken under the auspices of the assembly commission".
The letter also stated that Ch Supt Nigel Grimshaw  had "requested an immediate, updated threat assessment in relation to Parliament Buildings and will consider the findings upon receipt".
An assembly investigation into the flying of two unauthorised flags began after the incident, however, was later suspended due to the ongoing police investigation.
Contractors working at Parliament Buildings have been asked for a report by the assembly authorities.
The contractors are working on the site renovating parts of the roof and fourth floor.
The assembly said that the flags were removed as soon as it was made aware of them.
The PSNI has requested an "immediate, updated threat assessment" of the Stormont Assembly following an incident involving an Irish tricolour.