The revelation in the plans and priorities section of Finance Minister Jim Flaherty's March 29 budget also outlines delays in a string of other big-ticket equipment purchases at National Defence.
It comes as military procurement is under the microscope because of the politically charged F-35 project.
Originally ordered as part of sole-source contract with Boeing aircraft in 2006, the first Chinook is supposed to arrive next month, but it will be a test aircraft only.
The shortage of pilots is expected to delay bringing the Chinooks up to full combat capability until June 2017.
The helicopters were considered an absolute priority for the now-concluded combat mission in Afghanistan, but delays in buying the 15 new aircraft forced the Conservative government to spend nearly $300 million on six used Chinooks from the U.S. Army.
The surviving four helicopters from that batch, at last word, are up for sale and sitting at a military aircraft junkyard outside of Tucson, Ariz.
The pilot shortage is a matter of growing concern, to the point where the chief of the air staff recently told a Senate committee that Royal Air Force pilots were being imported to Canada to help with training.
The Defence Department was asked for facts and figures on the shortage and what happened to the pilots who flew the Chinooks in Afghanistan, but no one was immediately available to comment.
How much of the delays are related to the Harper government's deficit battle and what can be attributed to procurement snarls is unclear.
Another aircraft purchase that remains in limbo involves replacements for the country's fixed-wing, search-and-rescue fleet. The budget documents say the new planes won't arrive before in 2017.
However, the air force has repeatedly warned that its fleet of C-115 Buffalo search planes, now almost 50 years old, must be retired by 2015.
The replacement program has been mired in the bureaucracy after accusations that the air force rigged the specifications in favour of one aircraft, a claim mirrored in the ongoing F-35 debate.
The budget documents also show that Conservative's pet project of building Arctic patrol ships is being delayed. The first vessel won't arrive until 2018 — three years after initially promised — and won't be fully operational until 2023.
The replacement for the navy's two 50-year-old supply ships now is slated for delivery in 2018 — a decade after the Conservative government shelved the original program because bids exceeded the budget.
The NDP defence critic says the myriad of delayed programs are symbols of how the Conservatives view defence.
Jack Harris said the Harper government is more interested in looking tough on the international stage with missions such as Afghanistan and Libya, while domestic concerns are shoved to the back burner.
"Look at the choices they are making," he said. "We've got a mess within our own government.
"We've got example after example of the Department of National Defence not being able to line up their ducks in a row to be able to do the job they're supposed to be doing for Canadians."
Other delayed projects include the army's long-range rocket artillery system, which is now put off until 2019. The air force's plan to buy unmanned aerial vehicles is also stuck, with each project deadline marked with a "to be determined" notice.