At least 35 people were killed during the unrest between October 28 and January 11.
The deputy police commissioner did not give details of the exact role Hasina has been accused of playing in the murders.
The murder charge came after Hasina, who served as prime minister between 1996 and 2001, was accused on Monday of extorting 30m taka ($434,000 dollars) while in office.
Hasina's press secretary had said the opposition leader planned to cut short her visit to the US and return home on April 14 to fight the extortion allegations.
Murder charges have also been brought against 55 other political figures, including the leader of Jamaat-e-Islami, which was part of the four-party coalition government which handed over power last October in preparation for elections.
The parliamentary polls, planned for January, were cancelled after months of political turmoil over allegations of poll-rigging and the country was placed under emergency rule.
The murder charges were announced as Bangladesh's military-backed caretaker government severely curtailed the freedom of Khaleda Zia, the former prime minister who stood aside in October.
"The intelligence department sent the order to the guards at Zia's house that only four people could meet her from now on," the former prime minister's acting secretary said.
"They are her two brothers, a personal physician and an ex-member of parliament."
The secretary said he did not know if Zia's movements had also been restricted.
The military-backed government has said it will root out corruption and carry out sweeping political reforms before announcing a new election date.
There has been widespread media speculation that the government is seeking to force Hasina and Zia into political exile, but this has been denied by the administration.