He said he believes the number of strikers was lower than union estimates, but did not provide a figure.
President Susilo Bambang Yudhoyono called the strike unfortunate because it could discourage foreign investment, his spokesman Julian Pasha said.
Factory workers in Indonesia earn an average basic salary of just over $120 a month. The economy grew 6.5 percent last year, the fastest pace since the 1997-98 Asian financial crisis, and the cost of living has been increasing, making it harder for workers to pay for food and basic necessities.
Protests are common in Indonesia and are generally peaceful.