The 34-year old Socceroos captain was set to join the Heart late last week but decided to head back to his home city of Sydney at the last moment.
Many outsiders believe that Neill had been given a better financial offer by the Sky Blues but he insists that the move was simply for 'football reasons' and to re-settle in the New South Wales capital.
"I want to clear the air a little bit about the situation," Neill said. "I did give an indication I would be excited by the opportunity to go to Melbourne.
"There was never a case of leveraging one club against the other but the opportunity became very real to join Sydney. It was a difficult decision but was an easy one from a family point of view being born and raised in Sydney ... and exciting times here at Sydney FC to commit myself to this club.
"As far as being gazumped at the last minute, there was never a question of money. My intention is to come here for football reasons. We made that very clear that this wasn't financial.
"I think it's well documented that Melbourne's offer was for $100,000 and I've signed for $70k, so I think we leave it at that."
He added: "To the Melbourne Heart board and John Aloisi and Hayden (Foxe, assistant coach) I apologise if I gave too much of an indication I was heading down to Melbourne and I wish them all the best.
"In an ironic way I look forward to playing against them or some part this weekend in Melbourne."