A joint statement issued by several labour unions said a total of 80 industrial estates in 24 cities were impacted by the work stoppage.
The biggest demonstration took place in the capital, Jakarta, where more than 700 companies were closed down.
The Kyodo news agency reports that police deployed 11,000 officers and 4,000 military personnel to monitor protests in the city, and to "secure" rallies planned outside the Manpower Ministry, the State Palace and the House of Representatives.
Keeping local jobs
Said Iqbal, president of the Confederation of Indonesian Workers Union, said the workers want the government to stop outsourcing, which allows companies to terminate working contracts without compensation, by 15 October.
An earlier deadline to review the outsourcing and cheap labour laws has not been met.
Another labor representative interviewed by the Jakarta-based network tvOne said workers wanted the minimum wage increased.
"In Jakarta, to have a decent living, a worker must get a minimum wage of 3,750,000 rupiah (about 383 Australian dollars) a month, but we only get 1,529,150 rupiah (156 Australian dollars)," the representative said.
He said the situation was particularly tense since the issuing of a Health Ministry recommendation that workers share the cost of health insurance premiums with their employers.
"Our life has been miserable with the low wage, so why should we share payment of the premium? The companies must fully pay the premium," the representative added.