Claims that favoured people were being "parachuted" into Wales had led to anger among activists and resignations.
Speaking on a BBC Wales Ask the Leader TV programme, Mr Gill said the choice of candidates was down to party members and he himself "had no say".
But he said the former MPs were assets to the party with great experience.
"I am the leader of UKIP in Wales but I do not have a great deal of power with, and certainly not with regard to the selection of, candidates," Mr Gill said.
"The selection of candidates went to a ballot of the membership. The membership selected who they wanted in each region and the NEC approved that.
"I had no say in that whatsoever.
"Would I have allowed people to come in over our hardworking Welsh membership? Probably not... but it wasn't my decision.
"The members have given us these candidates and therefore I back them."
Mr Gill added: "Of course they've got years of experience.
"Mark Reckless was an MP. He did a very brave thing when he came over to UKIP. We all recognise that. He's a very intelligent and clever man.
"Of course they're an asset."
Asked about his leadership of the party in Wales, Mr Gill said: "There are lots of things that frustrate me about politics and certainly UKIP and the internal wranglings of the party, let's be perfectly honest.
"I've been quoted several times as saying it is like herding cats. I'm afraid that's because of all the different personalities.
"We're a bit of a fiery party."
Pushed on whether he would stay on as UKIP Wales leader after the referendum on Europe in June, Mr Gill said: "Absolutely."
On the subject of climate change, Mr Gill said he was "very, very sceptical" that mankind had any impact and insisted no money should be spent trying to tackle global warming.
"[We're] literally a bunch of people, King Canutes, thinking that we can stop the tide," he said.
"The most expensive piece of legislation in British history wasn't the First World War or the Second World War - it was [former Labour energy secretary] Ed Miliband's climate change act."
UKIP Wales leader Nathan Gill has said he would "probably not" have chosen ex-MPs Mark Reckless and Neil Hamilton as assembly election candidates.