The players left the athletes' village following their game against Qatar on Thursday to eat at a restaurant where they met a Japanese-speaking local, who told them about a bar where they could meet women, Yamashita told a news conference.
The quartet, who were wearing their team uniforms, spent a couple of hours at the bar before checking into a hotel with four women, staying there until Friday morning, he added.
Officials named the players as Takuya Hashimoto, Keita Imamura, Yuya Nagayoshi and Takuma Sato.
"The Japan Olympic Committee decided to withdraw their accreditation and send them back to Japan early this morning," Yamashita said.
"We have a specific disciplinary code, it's a clear breach of the code of conduct for the Japanese delegation. The athletes should be role models of society, not only in the sporting venues but also on other occasions."
Yamashita said the Japanese Olympic Committee took the issue of discipline in their team very seriously.
"A day after our arrival here the Chef de Mission and other top officials told the athletes that they had to be role models in Jakarta," he said.
"It's disappointing that after that instruction and encouragement, this kind of issue happened, I deeply apologise to the Japanese people as the head of the delegation."
Olympic Council of Asia (OCA) President Sheikh Ahmad Al-Fahad Al-Ahmed Al-Sabah later commended the JOC on their swift action and said athletes had a responsibility to set a good example at major sporting events.
"Athletes should be an example to society," the Kuwaiti told a news conference.
"To represent your country is not only to stand with medals but also in your dealings with other athletes, officials, volunteers and the people of the host country.
"I hope the Japanese and other athletes learn a lesson from this."
At the 2014 Asian Games in Incheon swimmer Naoya Tomita brought embarrassment to Japan when he was caught on surveillance cameras stealing video equipment from a journalist.
He was later fined by a South Korean court and banned from competition for 18 months by the Japanese swimming federation.
Japan, who won basketball bronze at the last Asian Games four years ago, beat Qatar 82-71 in their second game in Jakarta and top qualifying Group C. Their next fixture is against Hong Kong on Wednesday.
"The players flew back home at their own expense," Yamashita added. "The remaining eight players, officials and coaches will stay here to continue to play for the rest of the competition."
The next Olympics will be hosted by Japan in Tokyo in 2020.
(Writing by Nick Mulvenney; editing by Peter Rutherford)
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