Tonga's Minister of Transport Paul Karalus announced his resignation on Tuesday, six days after the sinking of a domestic ferry, Tonga media reported.
The Princess Ashika ferry, en route to the Nomuka Islands group, sank about 86 km northwest of the capital Nuku'alofa last Wednesday.
Ninety-three people remain unaccounted for and two bodies have been recovered.
The minister who is responsible for shipping and aviation, said he had tendered his resignation to Princess Pilolevu Tuita and Prime Minister Feleti Sevele, so that he can give his full support to the investigation of the Royal Commission of Inquiry into the sinking of the ferry, the Matangi Tonga online reported.
Karalus said that to enable the work of the Royal Commission of Inquiry to run smoothly he would not be talking about any matters relating to the Princess Ashika in public.
Karalus denied there were problems with the ferry's seaworthiness or that concerns had been raised with the government before the tragedy.
But anger has been increasing in Tonga as people demanding answers have packed churches across the nation to mourn the loss of their loved ones.
Work was under way to establish a Royal Commission of Inquiry and a special sitting of Parliament was held on Tuesday to work towards setting this up.
Karalus said his decision is not an admission of guilt, but rather a legal requirement.
In a statement on Tuesday, he said it is essential that a complete and full investigation into the tragedy be made as soon as possible, and that it be carried out thoroughly and transparently.
"Although I, as Minister for Transport, and my ministry and staff know that we have performed our duties with due care and diligence, the overall interests of Tonga must be taken into account at this difficult time," he said.
"It is for this reason that I have considered and taken the decision to resign from my ministerial post."
Bad weather in Tonga was preventing attempts by New Zealand navy divers to investigate a rope found rising from the seabed in the area where the ferry sank.
The wreck has not yet been located and an eight-mile exclusion zone has been established at the site.
The rope and visible oil are near where the ferry's emergency beacon activated.
Head of the Royal New Zealand Navy team, Andrew McMillan, said they want to re-deploy an automated undersea vessel to explore thearea but weather conditions on Tuesday mean that is doubtful.
Parts of the search area are more than 100 meters deep. McMillan said he believed there is no chance of people having survived inside the ferry.
The search for survivors is continuing.
The second of two bodies recovered so far has been identified. The woman, Vaefetu'u Mahe, 22, was from the remote Tongan island of Vava'u.