"But if hudud becomes a major issue, Pakatan may go the way of the previous Barisan Alternatif," Lim said in a statement on Sunday.
Barisan Alternatif was a group of Opposition parties formed to counter Barisan Nasional, which disbanded after the general election in 2004.
Lim, who is Gelang Patah MP, said should such a situation occur, then DAP, PKR and PAS would be the losers.
He said the majority of voters who supported Pakatan in the last general election did so for a change of government and not for hudud.
"Pakatan would not have continued to deny Barisan's two-thirds majority in Parliament if hudud was our agenda in the 13th general election," he said, adding that the DAP, PKR and PAS would have suffered serious electoral losses if hudud had been an issue back then.
PAS president Datuk Seri Abdul Hadi Awang is expected to move a Private Member's Bill at the Dewan Rakyat next month to pave the way for hudud to be implemented in Kelantan.
The proposal has been strongly opposed by DAP, which is PAS' ally in Pakatan Rakyat, as well as several parties in Barisan Nasional including MCA, MIC and Gerakan.
On April 24, Prime Minister Datuk Seri Najib Tun Razak said the Federal Government had never rejected the implementation of hudud but there were loopholes that needed to be addressed before it can be carried out.