The Indonesian Premier League (LPI) is an independent professional league launched last month without recognition from world governing body FIFA or the Football Association of Indonesia (PSSI), which has banned LPI players from representing their national team.
Ishak and Khaizan resigned from their PSSI-supported Indonesia Super League team Persib Bandung to join Medan Chiefs.
Zainudin Nordin, president of the Football Association of Singapore (FAS), said he understood the players' desire to maximise their earnings in what could be short careers but their decision came with risks.
"Both players have opted to play in a league which is not sanctioned by the country's football association," he said in a statement on Sunday.
"Depending on FIFA's ruling on the issue, Shahril and Baihakki may find themselves disqualified from playing for Singapore and possibly FIFA-sanctioned Leagues for a significant period of time.
"It would have been an ideal situation if the high salaries are paid by a club properly sanctioned by the Football Association of Indonesia."
The 19-team LPI, which includes three sides who switched from the ISL, is the brainchild of oil tycoon Arifin Panigoro. It is aimed at improving the level of the game in the country ranked 129th by FIFA and is backed by the country's sports minister.
The Singapore duo will become the latest names to join the league which has been on a high-profile recruitment drive following the capture of once-capped England international Lee Hendrie last month.
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