The 28-year-old risks being frozen out of Malaysia's national side by opting to stay in the controversial Indonesian Super League (ISL), local media reported on Thursday.
But Safee's agent brushed off the threat of sanctions, claiming his client had a "foolproof contract" despite the fact FIFA does not recognise the rebel league.
"The report that the ISL has been banned is not true," Zakaria Rahim told The Star newspaper. "His playing career is not under threat.
"In a worst-case scenario, if the ISL is banned, Safee has the option to join Pelita Jaya's sister clubs [in Indonesia] and abroad."
Safee signed a two-year extension with the team for two million Malaysian ringgit ($657,500), pocketing him a reported $30,000 a month, not including match bonuses.
It was a tough decision for Safee to make given that FIFA had ruled that players in the breakaway ISL would no longer be eligible for their national teams.
"I'm a professional player, which means I decide everything on my own," Safee told the Jakarta Globe. "Nobody can forbid me to play in the ISL."
The Football Association of Malaysia (FAM) had asked Safee to leave Pelita Jaya to avoid being banned for national duty.
FIFA is backing the Indonesian football association (PSSI) after also threatening them with sanctions last year following a damaging leadership election crisis.
A letter to the PSSI, signed by FIFA General Secretary Jerome Valcke, said a freeze had been imposed on the transfer of players from the ISL.
Football's world governing body have given Indonesia until March 22 to sort out its domestic problems, warning that failure to do so would result in harsher sanctions.
"FIFA have never banned the ISL," said Zakaria, pointing to a potential solution to a bitter row that has threatened to get Indonesia booted out of FIFA.
"PSSI are set to have a meeting on March 22 to decide the fate of the leagues and PSSI itself."
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