Local residents in nearby houses have been evacuated with their pets.
It is understood that the President remained in MacLeod House on the estate while officers carried out checks.
There are still people on the course and in the clubhouse.
Police Scotland initially released a statement to say the situation was over and the cordon had been lifted, but those in attendance said it was not the case.
Read More
The force has since issued a further statement to say the cordon does remain in place after military colleagues requested a further opportunity to check the vehicle that was the subject of the investigation.
A Police Scotland spokesperson initially said: “Shortly after 3pm, a security cordon was put in place at an entrance to the Menie Estate, Aberdeenshire, as officers carried out precautionary checks on a vehicle.
“This search has been completed, there was no criminality and the cordon has been removed.”
They later added: “As the cordon was being removed, military colleagues from EOD requested to carry out further checks on the vehicle.
“These remain ongoing and the decision has been taken to maintain the cordon at this time.”
A further update at 6.30pm said: “We have been advised by military colleagues in EOD that further searches of the vehicle have now been completed. “There is no risk and cordons are in the process of being lifted. It was a false alarm with good intent.”