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The left-leaning SDP, one of the junior coalition parties of the Hatoyama Cabinet, is opposed to the relocation plan and has persistently insisted the Futenma base be moved out of the southern island prefecture and preferably out of Japan all together.
For her part Fukushima said she was disappointed about the decision.
"The prime minister asked me to sign a document that was counter to the SDP's position of not relocating the Futenma facility within Okinawa," Fukushima said at a news conference.
"The SDP and I will not betray Okinawa. We will not continue playing a role in imposing a heavy burden on people in Okinawa," she added.
Despite saying the news of the agreement was "very disappointing", she said she planned to remain in the cabinet.
"I am not thinking about it at all," Fukushima told reporters, regarding her possible intentions of leaving.
The prime minister said that Chief Cabinet Secretary Hirofumi Hirano would temporarily take over Fukushima's ministerial duties.
In his national address, Hatoyama went on to say that he will seek understanding from the people of Okinawa and from members of the coalition parties before the upper house election in July, indicating he has no plans to step down to take responsibility for the confusion over the base issue.