The Fianna Fail leader says there needs to be a single 'comprehensive' inquiry into the death of Savita Halappanavar.
The Health Information and Quality Authority (HIQA) will decide today whether to carry out its own investigation following a request from the HSE, which is also looking into the case.
A spokesman for the Health Minister says the involvement of the health watchdog would provide 'even greater ventilation' of the issues at stake.
However the own investigation by the Health Service Executive (HSE) is to continue.
Its chief executive Tony O'Brien says the decision by Praveen Halappanavar not to co-operate with its inquiry does not absolve it of its duty to investigate her death.
He said it would be criminally negligent not to proceed with this investigation.
'One substantive inquiry'
Speaking to Breakfast here on Newstalk Micheal Martin called for an independent inquiry to be set up under the terms of the Commission of Inquiries act.
He says this would allow a speedy inquiry, procurement of documents and for witnesses to be compelled to give evidence.
"The Commission of Inquiry allows for a very speedy inquiry, it allows for compelability of witnesses - and procurement of documents" he said.
"And I believe that now is the kind of inquiry that would command the confidence of the wider public, and indeed of Praveen Halappanavar".
"I would not proceed with the other 2, you need 1 substantive (and) comprehensive inquiry" he added.
Elsewhere ahead of the report by an expert group on abortion going before the Cabinet next week reports today claim it does not point out how existing Irish laws could allow regulation for the 'X Case'.