The league statement came after The Associated Press on Monday highlighted the confusion over Lampard's status amid continuing silence by the teams.
The New York team, which debuts in Major League Soccer in March, announced last July that Lampard signed a two-year contract, and used it to promote the sale of jerseys and season tickets.
Shortly afterward, Man City said Lampard was returning to the Premier League on loan to stay match fit for his New York debut. But the announcement has been removed from the team website, and City never used the term "loan" again.
Lampard's seven goals have been valuable to the team's title defence, and when City announced on Dec. 31 that he was staying for the rest of the season, the team said his "contract" had been extended.
MLS told the AP that although Lampard had not signed a contract with NYCFC, the midfielder had one with City Football Group, the umbrella company for the portfolio of clubs owned by Abu Dhabi's Sheikh Mansour.
Now the Premier League has investigated the matter and confirmed that no integrity rules have been breached because Lampard's only contract is with Man City and he is not on loan.
"Frank Lampard is registered with Manchester City FC until the end of the 2014-15 season," the league said in a statement. "The Premier League has sought and received assurances from Manchester City that there is no agreement in place between the club or City Football Group with New York City FC relating to the player."
The 36-year-old former Chelsea player originally said he was moving to MLS because he "didn't want to play anywhere else in England because I had been so affiliated with one club."
There has been criticism in the United States over Lampard's failure to start the MLS season with the expansion franchise.
NYCFC supporters' group, The Third Rail, said it was "outraged" by Lampard's prolonged stay in England.
"Many fans, including our members, decided to support the team, committed to season tickets, and bought merchandise under the impression that Frank Lampard would be playing for New York City Football Club, not Manchester City," the group said.
Jan. 5 AP story on Lampard's contractual confusion: http://bit.ly/1tO0vd2
Rob Harris can be followed at www.twitte.com/RobHarris