The UAE and Saudi Arabia summoned Lebanon's ambassadors to protest against Information Minister George Kordahi's claim that Iran-backed Houthi rebels in Yemen were acting in self defence.
Mr Kordahi said during a television interview on Monday that the Houthis, who seized the Yemeni capital in 2014 and forced the internationally recognised government into exile, were "defending themselves ... against an external aggression".
A coalition of Arab nations intervened in the war in 2015 at the request of the Yemeni government.
The Saudi Foreign Ministry said on Wednesday that it handed the Lebanese ambassador a memorandum protesting against Mr Kordahi's "offensive" remarks.
It said the statements were "clearly biased towards the terrorist Houthi militia that threatens the security and stability of the region".
The UAE also summoned Lebanon's ambassador to express its "condemnation and dismay" over the statements.
Mr Kordahi's "disgraceful and biased" comments "offended the member countries of the coalition", the Ministry of Foreign Affairs and International Co-operation said in a statement carried by the UAE's official Wam news agency.
Amid international efforts to reach a political settlement to the conflict, the Houthis attacked the government-held city of Marib in February. The rebels have pressed their offensive despite UN calls for de-escalation over fears for the civilian population, including hundreds of thousands of people already displaced by the war.
Lebanese Prime Minister Najib Mikati said Mr Kordahi's statements "do not express the government's position at all", and reiterated his support for Saudi Arabia and the Gulf Co-operation Council.
The minister's comments place further strain on Lebanon's relations with traditional Gulf allies, which have deteriorated with the growing influence of the Iran-backed Hezbollah movement in the Lebanese government.
Mr Kordahi, a well-known television presenter, said he gave the interview on August 5 and the remarks were his "personal opinion".
"I did not wrong anyone. I did not attack anyone. Why should I apologise?" he told reporters in Beirut.