Prime Minister Lawrence Gonzi said his party's condemnation of MPs was a natural consequence of their actions.
Additional reporting by Miriam Dalli.
Updated with Nationalist MP Charlò Bonnici's comment at 11:37am.
Updated with Franco Debono's comment at 12:38pm.
Prime Minister Lawrence Gonzi did not rule out the possibility that MPs Jeffrey Pullicino Orlando, Jesmond Mugliett or Franco Debono could face some form of expulsion after not supporting government in two Opposition motions.
"It is an internal party matter for the PN to consider," Gonzi told the press when asked whether it was being considered to have the three MPs expelled.
Gonzi defended the party's executive committee's decision to issue a public condemnation of the three MPs.
"It's simple, the party has its democratic rules and the executive is a forum open to all MPs, open to them to defend their position. The meeting had been pre-announced and the MPs did not attend, and the executive explained the circumstances of the events that took place and a public decision was taken. This is the PN in its own democratic forum," Gonzi said.
The prime minister also said that MPs had to face any consequence to the decisions they take.
"They should know that this was a very serious matter that has now brought obvious consequences, and these are the very consequences," Gonzi said.
Backbencher Franco Debono together with backbenchers Jeffrey Pullicino Orlando and Jesmond Mugliett have been "condemned" by the PN executive council for how they voted separately in parliament.
Debono said he will be asking the PN's executive committee to nullify a decision to condemn his vote in favour of an Opposition motion that led to the resignation of home affairs minister Carm Mifsud Bonnici.
Debono insisted that he was unable to attend an executive committee meeting the party held to discuss the vote taken by Debono, as well as Jeffrey Pullicino Orlando and Jesmond Mugliett on Monday's motion that resulted in the resignation of Richard Cachia Caruana from permanent representative to the EU.
"The decision was not listed in the party meeting agenda and I was unaware of the discussion... nobody can take a decision on a person without being present for the meeting to defend oneself.
"I have informed the secretary-general that I want to ask for this decision to be annulled."
In a separate comment he posted on his personal blog, Nationalist MP Charlò Bonnici said the PN's decision was "quite soft" when considering the damage inflicted by the MPs' votes.
Bonnici said the party's decision meant the MPs' actions were "not business as usual... The lost votes in Parliament were surely a hard blow below the belt for the Party, so no one should be surprised that it has now reacted. After all the dissent has caused the resignation of a minister as well as an ambassador. Above all, the whole situation has embarrassed the Nationalist Party and it's members.
"If you tell me, I think the Party's approach has been quite soft when compared to the extent of the damage caused. But then I am neither the Party leader nor its secretary-general so I accept that sometimes one needs to see the whole picture rather than just a small part of it. At least with yesterday's press release the PN has sent a signal that no, it's not business as usual."
Debono had voted in favour of an Opposition which called for the resignation of former minister Carm Mifsud Bonnici, while Pullicino Orlando voted in favour of a motion that called for the resignation of Malta's permanent representative to the EU Richard Cachia Caruana. Mugliett abstained on this motion.
The Nationalist Party's executive committee met for the first time following the resignation of Mifsud Bonnici and Cachia Caruana on Thursday and issued a condemnation of the three MPs' votes, without explaining further what measures the condemnation involved.
The PN added that executive council also encouraged Cachia Caruana and Mifsud Bonnici to continue to work for the country "despite the personal attacks against them".
The PN's decision to highlight the "personal attacks" suffered by Cachia Caruana and Mifsud Bonnici highly contrasts with the statements made by Debono and Pullicino Orlando in parliament while justifying their voting intentions.
Both backbenchers in their speech had insisted that their vote "was nothing personal", with Debono insisting his vote was informed by the need to reform justice and home affairs, while Pullicino Orlando insisted that no one should be above parliament.