Soccer's world governing body would amend its rules to cover both matters, Blatter told a news conference after a meeting of FIFA's executive committee.
The issue of third-party ownership was brought to FIFA's attention during the protracted transfer of Argentine striker Carlos Tevez from West Ham to Manchester United earlier this year.
The Tevez case was complicated by the fact that the player's transfer rights were partly owned by a private company rather than just his club.
Although common practice in South America, the set-up breached Premier League rules and led to West Ham receiving a record 5.5-million-pound ($11.31-million) fine from the league.
Blatter said FIFA had also been unhappy about the case of Spanish fourth division side Granada 74 which succeeded in effectively purchasing a place in the country's second division from Ciudad de Murcia.
NEW RULES
The Spanish Football Federation failed to block the move after the Court of Arbitration for Sport (CAS) agreed with Granada that they had simply relocated and renamed an existing club.
"We are not happy with that decision which goes against the principles of our game where promotion and relegation is the essence," Blatter said.
"So we have changed the regulations and the new rules will be enforced at the end of the year."
Blatter also said FIFA would tighten up procedures for contracts involving its own employees, following the controversial departure of former general secretary Urs Linsi.
"We have had some expenses caused by some people in FIFA leaving our offices in unforeseen circumstances," he said.
"We have now put in barriers so that such a situation cannot be repeated, with (future) contracts now being audited by an internal office of compliance and external lawyers and then being activated only by the general secretary and the president."
A Swiss newspaper said in September that Linsi had received around eight million Swiss Francs ($6.89 million) from FIFA after signing an eight-year contract shortly before his dismissal.
