Unions that have been derecognised by QinetiQ are Prospect, GMB, PCS and Unite, which between them have thousands of members at the company's 40 sites across the country.
The accusation came from Mike Clancy, general secretary designate of Prospect, who called it "nothing more than crude union-busting."
Leo Quinn, chief executive of QinetiQ, took the drastic step in favour of giving staff a 'voice' on a newly-formed employee engagement group.
Clancy said unions in QinetiQ had always engaged constructively with the company on difficult issues such as redundancy terms and pension changes, yet were now being forcibly ejected because members voted against a controversial pay offer last year.
He warned: "It is clear the chief executive wishes to neutralise any potential challenge and drive through changes to terms and conditions without any moderation or consultation with unions.
"QinetiQ now stands out as the only major MOD contractor that has removed the right of its employees to be collectively represented by independent trade unions."
In the past QinetiQ had been happy to consult and seek agreement on the tough issues it has faced, he pointed out.
"We will campaign vigorously to maintain the union voice at the company. QinetiQ should listen to its staff. There has been no call for derecognition from them."
National secretary David Luxton said: "Members can be confident that the Prospect branch will remain active in QinetiQ. Prospect will be around long after Leo Quinn has left the company."
In three weeks since the announcement Prospect membership rose by more than 200 members, which Luxton called "a great boost to our campaign for statutory recognition.
"We are working closely with our legal advisors on the timing of our approach to the Central Arbitration Committee, the statutory body responsible for union recognition," he said.
- In March, QinetiQ announced that its defined benefit pension scheme was to switch from RPI to CPI for uprating purposes, despite specific assurances in 2008 that RPI would apply in return for higher contributions.