"We hereby give notice by KQ (Kenya Airways) of its immediate withdrawal from the existing recognition agreement and the collective bargaining agreement with KALPA," the company said in the letter.
The airline has warned the striking pilots they could be dismissed if they do not return to work immediately. It also started recruiting new pilots and to institute disciplinary action against those on strike.
The union did not respond when Reuters sought comment, saying its leadership was in court.
On Monday, a judge of the employment and labor court ordered 11 union officials to appear before her on Tuesday to explain why they disobeyed the court's orders, which restrained the pilots from starting the walkout.
The court Tuesday ordered the union and the airline to hammer out a resolution to the dispute.
Members of the Kenya Airline Pilots Association (KALPA) — a union that represents about 400 pilots at the carrier - went on strike on Saturday after failing to resolve a dispute over their pensions contributions and settlement of deferred pay.
The walkout led to the cancellation of dozens of flights and stranded thousands of passengers.