Hundreds of Roma "gypsies" have looted shops and clashed with police in the past week to protest against the government's benefit cuts.
President Schuster, who questioned the size and timing of the cuts, said they could lead to "wider social unrest".
The government said the situation had stabilised and accused the president of electioneering ahead of a March vote.
The unemployment problem is especially acute among the country's impoverished Roma community.
Correspondents say unemployment rates reach 100% in some villages.
Timing doubts
"I urge the government not to underestimate this social situation," Mr Schuster said.
"Nobody questions the need for reforms, but their size, timing and coordination are questionable."
He has also appealed for calm to the Roma community, who make up more than 8% of the population.
Dozens of Roma have been arrested in Slovakia since last week, when groups of Roma stormed shops in several eastern cities and stripped the shelves of goods.
An interior ministry spokesman said two police were lightly injured in the incident.
Private television TA3 reported that the unrest in Trebisov continued on Tuesday, and police used water guns to disperse people.
It said the government was considering sending reinforcements.
In reaction to the events, a Roma group cancelled nationwide demonstrations planned for Wednesday.
"The idea of showing the bad situation of Roma was abused," said Ladislav Fizik of the Roma Parliament group.
"Some militants mobilised Roma to loot shops - it is a delinquency we cannot accept."