The 13A, as it is called, was enacted in 1987 as part of Indian intervention to try and broker a solution to the Tamil demand for political autonomy.
The implementation of the 13th amendment is considered an important tool in achieving political reconciliation after years of conflict and bloodshed.
Minister of Housing Wimal Weerawansa, who leads the nationalist NFF, in a letter to Rajapaksa today warned that 13A has the potential to undo the achievements of government troops who defeated the LTTE.
He claimed that the amendment undermined the people's sovereignty and the supremacy of national parliament, and called for a national referendum to abolish it.
The issue surfaced as part of the reported unease between the judiciary and the executive arm of the state.
A financial bill which will purportedly usurp powers of the 13A and its embedded provincial council system was referred by the Supreme Court for approval of the provincial councils before being enacted in parliament.
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JHU or the Sinhala Heritage Party, another Rajapaksa ally backed the comments made by powerful defence secretary Gotabhaya Rajapaksa that 13A needs abolished.
"The TNA (main Tamil party) aims to target the 13A to further their separatist objectives," Udaya Gammanpila, the JHU senior and a Western Provincial Council minister told a public gathering today.
President Rajapaksa has earlier said that he was willing to consider granting full powers or 13 plus to the provincial councils.