At least one person was taken to a hospital after scuffles took place inside and in front of the Labor Ministry building. At least another two collapsed from the effects of pepper spray and were treated by other protesters on the spot.
The protest by a few hundred people was organized by a Communist-backed labor union. The government said damage was caused inside the office of the minister, Yianni Vroutsi, and threats made against the minister himself.
More than 30 protesters were detained, with further scuffles breaking out as the crowd attempted to stop the bus transporting them from leaving. Those detained were driven to police headquarters, with the demonstrators following on foot and protesting outside.
"Violence in all its forms must be condemned, not only in words but also by actions," government spokesman Simos Kedikoglou said. "The raid on the office of the labour minister, the material destruction and the threats against Yianni Vroutsi are practices which aim to dynamite the political climate at a very critical time for the country."
Greece has been gripped by a severe financial crisis since late 2009 and is being kept afloat by billions of euros in rescue loans from other eurozone countries and the International Monetary Fund. In return for the money, the government has imposed waves of spending cuts and tax hikes, leading to severe salary and pension cuts and leaving unemployment spiraling to above 26 percent.
Union members were protesting planned reforms to the pension and income contribution system - part of the latest spending cuts in the bailout program.
Other measures that took effect this year include a new 25 percent cut to the incomes of most public servants, leading to a string of new protests.
Public transport workers and hospital doctors are to hold a 24-hour strike in the capital on Thursday. Port workers start a 48-hour strike the same day which will leave Greek islands without ferry services. Other state-run services are also to be disrupted by work stoppages lasting several hours.
As the unionists clashed with police at the Labor Ministry, students at music schools were staging a separate demonstration in an adjacent square, ending with a free music concert.
Farmers in central Greece who are angry at higher taxes and other austerity measures have been parking their tractors by central highways as their unions decide whether they will set up roadblocks. Such farmers' protests in the past have completely blocked the highways, essentially cutting the country in two.
Last week, the government used emergency powers to force Athens subway workers to end rolling strikes that lasted eight days.
Striking workers at other transport services agreed to return to work this week, under the threat of more emergency action, but will push ahead with Thursday's strike.
The Brussels-based European Trade Union Confederation strongly condemned the action taken by the conservative-led coalition government, noting that workers who defy civil mobilization orders face prison sentences of up to five years.
"The wheeling out of emergency powers to enforce austerity policies is unacceptable," ETUC general secretary Bernadette Segol said in a statement.
Derek Gatopoulos in Athens and Raf Casert in Brussels contributed.