Baba Ramdev says he is on a "fast unto death" against corruption But Mr Singh justified the move, saying there had been "no alternative".
Police in Delhi broke up the yoga guru's fast over the weekend after angry exchanges with the authorities.
About 30 people were injured as police fired tear gas to disperse thousands of his supporters. An injured woman supporter is in a critical condition.
Civil society groups and leading anti-corruption campaigners have condemned the police action against Baba Ramdev and his supporters.
In his first remarks on Sunday night's incident, Mr Singh told reporters: "It is unfortunate that the operation had to be conducted, but quite honestly, there was no alternative."
He said the government was "serious" about tackling corruption, but there was "no magic wand".
The main opposition Bharatiya Janata Party has criticised Mr Singh's statement, saying it was "insensitive".
"It is [an] unfortunate, unexpected and bizarre statement made by the prime minister. It's inhuman, insensitive and complete carelessness on the part of the government," BJP spokesperson Rajiv Pratap Rudy said.
Separately, the Supreme Court has directed the government to explain the circumstances leading to the crackdown at Ramlila Maidan in Delhi, where the yoga guru and his supporters were fasting.
"The brutal force that was used by the police to disperse innocent people who had gathered at the Ramlila Maidan in furtherance of the permission granted by the state is a matter of concern for the court," the court said.
The government has justified the crackdown on Baba Ramdev's hunger strike, saying he had reneged on his promises during negotiations.
Baba Ramdev has vowed to continue his hunger strike against corruption in his home city of Haridwar. He wants suspected bribe money allegedly held overseas to be returned to India.
Baba Ramdev, whose daily TV programme is watched by millions, was detained by police on Sunday night and then sent out of Delhi.
He has called the police action a "blot on democracy and a conspiracy to kill me".
His protest comes as the Congress-led Indian government is struggling with a corruption scandal surrounding the sale of mobile phone operating licences.
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