The issue of bases in Okinawa has been an ongoing issues for years, with many residents saying they contribute to noise and crime.
Abe’s government, meanwhile, has been trying to move forward with plans to relocate the base from land that was reclaimed from waters near the town of Henoko in northern Okinawa.
But Onaga ordered a halt to underwater survey work; his government says the survey is damaging coral reefs.
The base is currently located in a heavily populated area, and the government wants to move it to what it consider to be a more ideal location.
Tensions between the two leaders came to a head on Friday when the two leaders met for the first time since Onaga was elected.
Onaga contends the base should be moved outside of Okinawa, and he has the support of several hundred residents who protested outside the meeting, some holding placards that said "Keep Your Dirty Hands Off Henoko."
Abe, on the other hand, said relocating the base to Henoko makes the most sense, but Onaga says he has the support of residents and will fight to stop it from going to the Okinawa region.
Abe is set to meet with President Obama in Washington on April 28, and the situation with US military bases in Okinawa is expected to be one of the key topics of discussion.