Carrying slogans and banners crticising the government, the marchers accused President Benigno Aquino of reneging on his campaign promise last year to raise the living standards of the country's workforce.
They also demanded an end to the government's policy of sending workers overseas an estimated nine million Filipinos work abroad and their millions in dollar remittances have traditionally buoyed the economy.
"All of Aquino's announcements are literally 'spare change' to appease workers," said Vencer Crisostomo, chairman of the group Anakbayan, after Aquino ignored a demand for a nationwide increase in monthly minimum wages.
"For the past several years, the government has always made a show of holding Labor Day job fairs. But why do many Filipinos still go overseas to look for greener pastures, even at their own risk?
It's because these job fairs do not solve the problem of low wages in locally based jobs."
The largest May Day protest took place in Manila, but there were also marches in major cities in the central and southern Philippines.
Aquino, in his labour day message, insisted the government was not deaf to the demands of workers, but stressed the country's poor fiscal position made it diffiult to quickly deliver on his promises.
He noted that the government had already announced non-wage benefits, including subsidies and allowances for the poor.
"We all know that the government lacks funds. But while we have limited funds, we have not been remiss in using them properly," Aquino said.
He urged the Filipino labour force to remain patient, and told them problems relating to jobs would not be solved overnight.
"Those who are telling you that lasting changes can be made overnight or in a month are only pulling your leg," he said.
"What is clear is that we are headed to real, significant changes."