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This is despite a National Party spokesperson telling media that the petition was "archived some weeks ago" as part of "normal web maintenance".
Speaking to media this morning, Bridges said when that comment was made to The Spinoff website yesterday, it was his understanding that this had been the case.
"What had actually happened, I have learned this morning, was that a junior staffer was incredibly emotional on Friday night and took it upon themselves to delete it – we didn't know that until this morning."
Asked if that was the right decision, Bridges said: "Honestly, I don't know".
"The reality is that we're not going to be critical of it because, as I say, it was a junior staff member who was very emotional."
The petition would not be put back up, he said – "what's done is done".
National campaigned strongly against the compact.
The petition, now deleted, said that the compact "defers our immigration policies to the UN. It also restricts the ability of future Government to set immigration and foreign policy, and to decide which migrants are welcome and which aren't".
Bridges this morning said National's comments on the compact were "legal points around New Zealand determining its law."
"If you look at our immigration position, I think we have the strongest pro-migration position across the Parliament."
The man charged with murder after the terror attacks on Friday had posted pictures of his gun on social media with apparent references to the Migration Compact written on the firearm.
Bridges said National regularly archived petitions.
"I'm not involved in website maintenance – it's not something I give a moment's thought in my role as leader of the National Party."