The airline said it had failed to agree a deal by the deadline imposed by the Australian government 21 days ago.
It will now have to accept an arrangement imposed by Fair Work, Australia’s industrial umpire.
The dispute between Qantas and the three unions that represent its staff centres on plans to cut Australian jobs and recruit cheaper staff from overseas.
The government stepped in last month after the airline grounded its entire fleet following a raft of crippling strikes.
Anil Lambert, a spokesman for the Australian and International Pilots Association said: “We thought a negotiated outcome was possible, but they [Qantas] turned that down.”
A spokesman for the airline said: “Qantas rejects claims that it terminated negotiations”.
Qantas is desperate to lower its cost base, which it says is as much as 20 per cent higher than its competitors.