Police said the incident happened at a filling station in Aughnacloy after 6am this morning.
The armed men threatened security staff who had been in the area attending to a cash machine before taking the money and making off from the scene in a dark coloured vehicle.
In an update police said the incident had been “shocking experience” for the staff involved, and appealed for dash-cam footage to help the investigation.
They added they are working alongside An Garda Síochána.

Armed robbers wearing boiler suits and masks stole money from a security van in County Tyrone. Photo: Pacemaker
Detective Inspector McCamley said: “All information relating to this armed robbery is needed. This would have been a shocking experience for the staff involved.
“This masked group had ordered staff into the ATM bunker then removed cash boxes from the security van and the cash machine.
“They then made off from the scene in the direction of Armagh in a dark-coloured Audi Q7 with a significant sum of cash. As part of our enquiries, we are liaising with An Garda Síochána.
“We are asking anyone with information or who may be able to help with our investigation to call us on 101 quoting 191 08/10/25.
“If you noticed any suspicious behaviour in and around this filling station in recent days or if you were travelling in the area at this time, we want to hear from you.
“Similarly if you have dash-cam footage covering this area or live in the general area and may have a doorbell camera, your information could be valuable to our investigation.”
Sinn Fein Fermanagh and South Tyrone MLA Colm Gildernew branded it as “disgraceful”.
Mr Gildernew added: “I want to strongly condemn it.
“My thoughts are with the workers caught up in it, who will no doubt be left frightened. Anyone with information should contact the police.”

The scene of the robbery in Aughnacloy.
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Ulster Unionist MLA Diana Armstrong added: “This was a brazen and deeply disturbing attack on those simply going about their daily job.
“It’s very shocking to hear of the use of firearms and threats to life in the quiet community of Aughnacloy.
“It is a relief to hear that no one was harmed or injured. I urge anyone with information to come forward to the PSNI immediately”.
“My office is liaising with the PSNI team in south Tyrone.”
Earlier today, PSNI Chief Inspector Ryan McConville said: “It was reported at around 6.40am that a short time earlier a group of males, wearing boiler suits and masks, armed with suspected firearms threatened security staff who had been attending an ATM at the premises on the Caledon Road.
“The group ordered staff into the ATM bunker then removed cash boxes from the security van and the ATM before making off from the scene in a dark coloured vehicle, with a significant sum of cash.”