Safee was halfway through a two-year contract with Pelita Jaya FC in the Indonesia Super League (ISL), which is not recognised by the All-Indonesia Football Association (PSSI), who notified the Malaysia Football Association (FAM) of the ban.
"We received a letter from PSSI (dated October 5) on Wednesday informing us of the status of the suspended clubs. Upon checking with the PSSI secretary, he told us that Safee's name was on the list," FAM secretary general Azzuddin Ahmad told the Malaysian Star on Friday.
"This is in line with a directive by FIFA that players and clubs in the illegal ISL will be barred from FIFA competitions and not allowed to play for their national teams.
"I won't know how long the ban is... but from what I gather the suspension is until PSSI hold their next congress in December," he said.
If Azzuddin is right, the ban would mean Safee would miss Malaysia's defence of the AFF Suzuki Cup, a hugely popular regional tournament for teams in Southeast Asia.
Safee, whose contract is worth two million Malaysian ringgit ($652,100), scored five goals and won the golden boot as Malaysia took the title two years ago.
They begin the defence of the crown on Nov. 25 in the eight-team tournament they are jointly hosting with Thailand.
The Malaysians beat Indonesia over two legs in the final in 2010 but the runners-up have endured a difficult period since with arguments over the running of the PSSI leaving them close to a ban from world governing body FIFA.
Organisers of a breakaway league were later voted in to take control of the PSSI making the new tournament official and discarding the original ISL as illegal.
The national team reached their nadir in February when they suffered a record 10-0 defeat by Bahrain in a World Cup qualifier after they were forced to hand debuts to a number of inexperienced players with many regulars blocked because of the ban on ISL players.
The issues were thought to have been resolved with a September meeting bringing the two warring factions around the table to thrash out plans for a new league combining teams from both sides in a new tournament for next year.
PSSI secretary general Halim Mahfudz said that despite the agreement, the ban on ISL clubs remained and was now extended to players of other national teams and not just Indonesia.
"The agreement is about uniting the leagues. The suspension of the ISL clubs is a separate issue that can only be resolved at the (PSSI) congress," Halim was quoted as saying by Indonesian media on Thursday.
