Chief executive Richard Scudamore says the Premier League has learned lessons from the Carlos Tevez saga.
Tevez joined West Ham with Javier Mascherano on 31 August 2006
Tevez, 23, completed a protracted move from West Ham to Manchester United on Friday after a dispute over the economic rights to the Argentine.
"West Ham have admitted that they were not clean and open with us last August when they signed Tevez," Scudamore told BBC Five Live's Sportsweek programme.
"We will have to be more circumspect when dealing with clubs from now on."
West Ham were fined £5.5m in April over the signings in August 2006 of Tevez and Javier Mascherano, who has since joined Liverpool.
The club was found guilty of acting improperly and withholding vital documentation over the duo's ownership.
West Ham said they had torn up the third-party agreement with the Tevez camp and re-registered Tevez for their last few games of the season, during which he helped keep the club in the Premier League.
His move to Old Trafford took so long because Media Sports Investment (MSI) and Just Sports Inc, who own the player's economic rights, and West Ham, who held his registration, fell out over how much compensation the club would need to release him.
They agreed on Friday that West Ham will receive a £2m fee for Tevez's registration - a move that was approved by the Premier League.
Scudamore says the League has tightened its rules and is working closely with the clubs to make sure problems do not arise again.
We run a league, not the country. There is a place where our job ends and the government's job starts
Richard Scudamore on the 'fit and proper person' test
He added: "We work with all the clubs to make sure deals comply and sit within the rules.
"We've changed the rules this summer so that the clubs are in no doubt that they must send any documentation surrounding any deal whether they think it's relevant or not.
"We want them to let the people who guard the rules make the decisions and decide what they need.
"We have also said that within that player's contract registration section that we will be taking into account rule U18 - the offending rule in the West Ham case - and rule U6 - another dual interest rule."
Meanwhile, Scudamore has defended the League after Manchester City owner Thaksin Shinawatra passed its 'fit and proper person' test.
Leading human rights organisations Human Rights Watch and Amnesty International expressed grave concerns about Thaksin in a BBC Five Live investigation, aired on Tuesday.
But Scudamore said: "We run a league, not the country. There is a reasonable place where our job ends and the government's job starts.
"If the UK government tells us that there is no problem then I don't think it is for us to go around second-guessing.
"If they tell us that x or y or z is not suitable to have investment in this country then they would stop the flow of money and we would work with them on that basis.
"Until then, you have to go along and administer the rulebook as described."