Cohen earlier rejected a House intelligence committee request for information.
Flynn's lobbying firm, Flynn Intel Group, was also subpoenaed, as was Cohen's firm, Michael D. Cohen & Associates.
Reps. Mike Conaway and Adam Schiff, who are leading the committee's probe, say the panel approved the subpoenas to compel certain individuals to testify and to obtain personal documents and business records. "We will continue to pursue this investigation wherever the facts may lead", they added. The subpoenas were part of seven total issued by the panel Wednesday; the other three relate to the alleged politically motivated unmasking of Trump campaign officials in intelligence reports, the Wall Street Journal reports.
Cohen is one of several Trump associates under scrutiny in a Federal Bureau of Investigation examination of contacts between Trump's campaign and Russian Federation, according to the New York Times.
Flynn was sacked by Trump in February after revelations that he misled administration officials about his contacts with Russia's ambassador.
Cohen told ABC on Tuesday that he "declined the invitation to participate, as the request was poorly phrased, overly broad, and not capable of being answered".
While Flynn has been a known target of congressional and Justice Department investigations into possible collusion between Moscow and the Trump presidential campaign, Cohen has only recently become a focus of the probe, for unknown reasons.
The three agencies were asked to provide records of any requests to "unmask", or reveal, names of Trump's associates by President Obama's former national security advisor, Susan Rice, former CIA Director John Brennan and former U.S. Ambassador to the United Nations Samantha Power, according to an aide familiar with the requests.
The subpoenas related to unmasking requests were reportedly made by Republicans on the committee interested in examining whether the requests were politically motivated, The Journal reported.
Meanwhile, Cohen, Trump's personal attorney, told the AP that he turned down a request for information from the House intelligence committee looking into the Russian interference.
Meanwhile, former Federal Bureau of Investigation director James Comey has been talking with Mueller about his intention to testify publicly - possibly as early as next week- before the Senate Intelligence Committee about his communications with the president.
Public testimony by the former FBI director could mark another major development in the controversy engulfing the Trump administration about past contacts with Russian officials - and whether the president or White House officials took steps to try to squelch the investigation.
Later in the day, the president re-tweeted a message from Fox News's Fox & Friends morning show that linked to a news article lacking an author and citing one unnamed source who challenged details of the Post's reporting.