The new Air Force One deal was a bad one for Boeing, according to the plane-maker's chief executive.
The firm said it expected to lose over a billion dollars on the two planes for the White House.
The company was forced to modify its contract by Mr. Trump.
Boeing was responsible for changes to costs under the new agreement.
We took some risks not knowing that Covid would arrive and not knowing that inflation would take hold like it has, and both of those have impacted us fairly severely.
Air Force One is a call sign for any aircraft carrying the US president.
The term refers to the current fleet, which has two highly customised Boeing 747-200B jets, which have been in service since 1990.
The government had a $4 billion contract with Boeing to build two or more new planes before Mr Trump was elected. Shortly after Mr Trump won the election, he called for the cancellation of the order because they were too expensive.
Two years later, the two sides announced a new $3.9 billion deal to convert two new 747-8 planes with a communications suite each, internal and external stairs, large galleys and other equipment and modifications to protect passengers.
Critics said the savings weren't clear, but Mr Trump hailed the agreement.
Boeing faced a very unique negotiation, a very unique set of risks that it probably shouldn't have taken during the Air Force One talks.
We are going to deliver great airplanes, but we are where we are.
The planes are designed to be airborne White House, able to fly in worst-case security scenarios, such as nuclear war, and are modified with military avionics, advanced communications and a self-defence system.
According to reports, the planes are behind schedule. Boeing has lost $660m on the programme.