Trump said the "tremendous cost and cost overruns" of Lockheed Martin's F-35 program led him to asking Boeing to "price-out a comparable F-18 Super Hornet."
Lockheed Martin shares fell about 2 percent, while Boeing shares were up 0.5 percent. Trump's tweet shaved off about $1.2 billion of Lockheed Martin's market value.
"We have committed to working with the president-elect and his administration to provide the best capability, deliverability and affordability across all Boeing products and services to meet our national security needs," Boeing told CNBC in a statement.
A spokesman for Lockheed Martin declined to comment to CNBC.
The president-elect previously threatened to cancel the order for a new Air Force One from Boeing because of the costs. He's also criticized the price of Lockheed Martin's F-35 program before, which took as much as $4 billion off of the company's market value.
The tweet comes after Trump met with the CEOs of both companies at his Mar-a-Lago resort in Florida on Wednesday. After meeting with the president-elect, Lockheed Martin CEO Marillyn Hewson said she "appreciated the opportunity to discuss the importance of the F-35 program and the progress we've made in bringing the costs down."