In a letter signed by Internal Affairs Minister Mr Jeje Odongo on Thursday, Mr Vanhelleputte, a Belgian, is to stay outside Uganda indefinitely.
Police spokesman Fred Enanga said Vanhelleputte had already been taken to Entebbe airport. "He's already at the airport and destined for Belgium around midnight. Over similar circumstances of national security," he said.
Last month the domestic intelligence unit in quick succession, rounded up and deported three top executives of the telecoms firm from Uganda between January 19 and 22.
The French nationals were MTN Uganda chief marketing officer Olivier Prentout, Rwandan Annie Bilenge Tabura, head of sales and distribution and the general manager for mobile financial services Elsa Mussolini who is French Italian.
Elsa Mussolini said at the time that she had been accused of inciting violence and funding the Ugandan opposition politician, Bobi Wine.
The musician turned politician is a critic of President Yoweri Museveni.
The South African-owned MTN has appointed the chief technical officer, Gordian Kyomukama as the company’s CEO in an acting capacity.
In a statement, MTN said it has not been notified of the grounds for Mr Vanhelleputte's deportation.
“We are understandably concerned about these developments and are engaging with the authorities to seek understanding that would lead us to resolving this matter,” the telecom said.