The Japanese government is under pressure to tighten its purse-strings on supporting some 50,000 American soldiers based in the country.
Japan is the only host country to subsidise the costs for US bases with a budget of billions of dollars a year.
It has allocated 217.3bn yen ($1.98bn) until March 2008.
'Show of consensus'
Kazuo Yamakawa, the union's chairman, said the strike was to demonstrate "a consensus among base workers that we cannot accept one-sided, disadvantageous changes to our working conditions".
Most of the strikers were restaurant workers, cleaners or housing maintenance staff on the bases, reported Japan's Kyodo News agency.
A Japanese defence ministry official said the strike will have some effect on the bases' operations but declined to immediately comment on the scale of it, citing possible ramifications on US-Japan relations.
Tsuneo Teruya, the union's secretary-general, said the action was the first nationwide strike at US bases in Japan since 1991.
A US military official said the strike had did not affected critical operations at the bases.