A federal investigation of Gov. Andrew Cuomo’s Buffalo Billion and upstate nanotech economic development initiatives has turned up suggestions of “improper lobbying and undisclosed conflicts of interest,” the administration revealed Friday afternoon.

While the statement from the governor’s counsel Alphonso David mentioned no names, it was issued just minutes after the Daily News reported that Joe Percoco, a former top aide to Cuomo, was a subject of the investigation along with Alain Kaloyeros, president of Albany-based SUNY Polytechnic Institute.

A source with knowledge of the situation said that the Cuomo administration had on Friday received a subpoena for documents related to the development projects from the office of U.S. Attorney for the Southern District Preet Bharara. The source said no current member of the administration had been subpoenaed.

David’s statement said Cuomo had ordered “an immediate full review” of the Buffalo Billion program, to be conducted by independent investigator Bart M. Schwartz, who formerly served as chief of the criminal division of the same U.S. Attorney’s office under Rudy Giuliani.

“Any grants made by this program will be thoroughly scrutinized — past, current or future,” David said. “ … Ensuring the integrity of the contracting process for this program is paramount, so that the Buffalo Billion and Nano program can continue creating new jobs and revitalizing Upstate’s economy.”

In a statement released along with David’s, Schwartz said the state “has reason to believe that in certain programs and regulatory approvals they may have been defrauded by improper bidding and failures to disclose potential conflicts of interest by lobbyists and former state employees. The U.S. Attorney has an ongoing investigation that has revealed important information in this regard. … The administration has made it clear to me that they have zero tolerance for any violation of the public trust from any actor or entity and I should follow the facts.”

The Daily News, citing unidentified sources, said the investigation also included lobbyist Todd Howe, Buffalo developer Louis Ciminelli and an energy company called Competitive Power Ventures.

Howe is president of WOH Government Solutions, a Washington, D.C.-based subsidiary of the Capital Region law firm Whiteman Osterman & Hanna LLP. Before entering the private sector, Howe worked under the governor’s father, former Gov. Mario Cuomo, and as a deputy to Andrew Cuomo during his tenure as the U.S. Department of Housing and Urban Development under President Bill Clinton.

An administration source said all contact with Howe and his firm are now off-limits for members of the administration and executive agencies. Howe did not respond to an email seeking comment.

Ciminelli is a principal in the construction firm developing the $900 million RiverBend solar panel factory that’s the centerpiece of the Buffalo Billion portfolio of projects. Previous reports said Bharara’s office was examining whether a competitive contract proposal was tailored to the company’s specifications, though the administration insisted the matter was a mere error. In March, the LPCiminelli firm hired Whiteman Osterman & Hanna to a $55,000 lobbying contract, according to documents filed with the state Joint Commission on Public Ethics.

Competitive Power Ventures develops and manages power generation projects, including a 1,080-megawatt plant in Athens, Greene County. It touts a clean-energy strategy focusing on electricity generated by wind power and natural gas.

SUNY Polytechnic, which is based in Albany but has developed a string of satellite campuses, received its own subpoenas from Bharara’s office in September. Kaloyeros, who has served as the point man for Cuomo’s high-tech endeavors, declined to comment Friday evening.

None of those men, however, are as close to Cuomo as Percoco is, or was.

Until he departed the administration just months ago for a job with Madison Square Garden, the broad-shouldered executive deputy secretary was among Cuomo’s most intimate aides — almost closer to a brother than a factotum. At Mario Cuomo’s January 2015 funeral, the governor referred to Percoco as “my father’s third son, who I sometimes think he loved the most.”

At the Capitol, Percoco would be tasked with everything from arranging the VIPs in a group photo at a bill signing to calling up recalcitrant lawmakers as a controversial bill was coming up for a vote.

No job was too sensitive: In July 2014, the Times Union reported that Percoco had been recruiting former members of Cuomo’s disbanded Moreland Commission to Investigate Public Corruption to issue statements defending the panel’s work. At the time, Percoco was on leave from the Executive Chamber to work for the governor’s re-election campaign.

A Wall Street Journal story published just days ago noted that Percoco continued to serve as the governor’s shadow at numerous public events, including the recent Democratic presidential debate in Brooklyn, despite the fact that he worked for a company with significant matters before the state.

The subpoenas issued to the Cuomo administration appear to be the governor’s first from Bharara’s office.

The U.S. Attorney for the Southern District has cut a wide swath through Albany over the past 16 months, beginning in January 2015 with the arrest of former Assembly Speaker Sheldon Silver and continuing with the arrest of ex-Senate Majority Leader Dean Skelos three months later. Both men were convicted of multiple public corruption felonies at the end of last year, and are scheduled to be sentenced in the coming weeks.

More recently, Bharara’s office has been one of the entities investigating New York City Mayor Bill de Blasio’s coordination of donations to Democratic Senate candidates during the 2014 election cycle. The state Board of Elections Enforcement Counsel Risa Sugarman concluded in January that sufficient evidence existed to suggest that de Blasio and his political and mayoral team worked to make an end run around campaign finance limits in their attempt to swing the Senate to Democratic control.

Here’s the double-barreled statement released from Cuomo’s administration: