An official source said the Indian statement issued after Nasheed walked into the Indian High Commission in Male Wednesday was never meant to "pass a judgement on their internal system".
"We have clarified our position (on the situation in the Maldives)," the source said, amid reports that the Indian High Commission website had been hacked.
The clarification came two days after India voiced concern over the "ongoing political instability" in the Maldives as Nasheed sought shelter citing possible imminent arrest.
The Indian statement had also urged the Maldivian government and political parties "to adhere strictly to democratic principles and the rule of law, thereby paving the way for free, fair, credible and inclusive elections".
The Maldives accused India of undermining its democratic institutions.
Indian External Affairs Minister SalmanKhurshid spoke for some 40 minutes with his Maldivian counterpart Abdul Samad Abdullah Thursday.
He stressed that India would like to see "free, fair, credible and inclusive elections leading up to a stable, peaceful and prosperous Maldives".
He said India would be happy to work with the Maldives to facilitate "this objective".
Abdullah told Khurshid that the Maldivian government "would do its utmost to prevent any precipitate act that adversely affects the atmosphere for a free and fair democratic process and rule of law".
The official source also explained the circumstances under which Nasheed came to the Indian mission Wednesday.
The source said the former president wanted to meet Indian High Commissioner D.N. Mulay. As the envoy was not there at that time, Nasheed decided to wait for him.
"He said he won't budge till he (Mulay) came..."
The official added that the political situation in the Maldives "can only be resolved when you have an elected government".
The official said that the warrant of arrest against Nasheed "has expired and he is free to go".
Nasheed has to deal with domestic issues, he said, and clarified that New Delhi "had no intention of getting drawn in, but Nasheed walked in..
"We have explained we were not interfering."
Maldivian press secretary MasoodImad told CNN-IBN Friday that while "India is the most important country for us to maintain the best of relations and we are continuing to do this", they wanted India "out of this and stay out of this issue and look at it as a judicial issue".
"This is Nasheed's drama and he has involved the Indian government in this for no reason at all. He has proved he can hold the Indian government hostage and involve the Indian government beyond rationale."
He said that none of Nasheed's problems "have been forwarded to us as something to negotiate or talk about. All we know is that he went to meet Mulay and is refusing to come out...
"Unless he decides to come out what do we do, it is none of our business."
UN Secretary General Ban ki-Moon has urged political actors in Male to "exercise restraint" and "work toward creating conditions conducive for fair, peaceful and inclusive" presidential elections due Sep 7.
Nasheed felt that if he was arrested and convicted, he could be prevented from contesting the presidential poll.
The first democratically elected president of the Maldives, Nasheed quit Feb 7 last year following what he alleged was a coup. He was succeeded by Vice President Mohammed Waheed Hassan.