The Ulster Unionists are claiming that the position of three DUP MPs is "completely at odds" with Arlene Foster's on a statute of limitations for soldiers who served in Northern Ireland.
UUP MLA Doug Beattie called on the DUP leader to explain her party's stance and repeated fears that a statute of limitations could lead to an amnesty for paramilitaries.
But the DUP last night accused its rival of making "disingenuous claims" and insisted that it supported "an end to the persecution of security force personnel" while opposing a general amnesty.
The dispute unfolded as talks to restore power-sharing continued at Stormont.
A source said dialogue yesterday between the DUP and Sinn Fein had focused on "the sustainability of the institutions so further collapses can be avoided". He added: "Reforms around this shouldn't be feared, but should be seen as laying a better foundation for future generations."
Mr Beattie said he was alarmed that DUP MP Gavin Robinson was continuing to support a statute of limitations and that the names of MPs Emma Little-Pengelly and Jim Shannon remained on a Bill being brought before Westminster.
He claimed the three MPs' position was in conflict with that of their leader, who had expressed concern in November about the potential implications of a statute of limitations for military personnel involved in Operation Banner - the British Army's operation in Northern Ireland from 1969 to 2007.
Legal advice suggested a statute of limitations would lead to a general amnesty "which would allow those responsible for some of the worst human rights abuses in our recent history to escape justice, or indeed the threat of justice", he said.
"Such an amnesty would also give terrorists equivalence with those who stood between the terrorists and the terrorised - our brave security forces - and that would be unacceptable," he added.
"Having called for the DUP leader to bring her MPs into line, it is now absolutely clear she does not have control over her party.
"Again we call on the DUP leader to explain her party's position on a statute of limitations, given the legal evidence and advice in the public domain. If she remains concerned - as we are - that it will lead to an amnesty, then she should instruct her MPs accordingly."
However, Sir Jeffrey Donaldson insisted DUP MPs had made it clear this week that they wouldn't "support an amnesty or anything which would preclude access to justice".
He said: "We make no apology, however, for wishing to end the unfair persecution of security force personnel who, having been investigated and cleared, can find themselves hauled before the courts years or even decades later.
"This point was again made by Gavin Robinson in Parliament this week, yet conveniently ignored by some in their chase to attack the DUP.
"We are deeply disappointed that the UUP are once again unwilling to support moves to place a clear time limit on prosecuting soldiers and police officers in circumstances where they have been properly investigated and cleared."
The Lagan Valley MP added: "Whilst we have concerns about how statute or limitations could be misused, we are open to a consultation on the matter where everyone can have their views heard. Why does Doug Beattie oppose this?"