A multi-storey church hostel collapsed last September in Lagos killing 116 people, many of them South Africans.
The authorities said it had more floors than its foundation could hold.
"The church was culpable because of criminal negligence resulting in the death of the victims," coroner Oyetade Komolafe said at the inquest in Lagos.
Mr Komolafe said Mr Joshua's Synagogue, Church of All Nations (SCOAN), had not obtained proper approval before putting up the structure.
Those who built the hostel should also be investigated, he said.
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TB Joshua, referred to by his followers as a "prophet", had blamed last year's incident on a small plane which he said had been circling the building, a claim dismissed by the court.
Straight after the building collapsed, emergency teams complained that church officials had blocked access to the site.
The coroner also criticised the fact that the preacher had not appeared as a witness during the inquest.
"Among the individuals and organisations summoned, only Prophet TB Joshua refused to testify," the AFP news agency quotes Mr Komolafe as saying.
The BBC's Will Ross in Lagos says the preacher went to another court arguing that the coroner did not have the right to summon him.
Mr Joshua's services, at a mega-church in Lagos's Ikotun district, are known for attracting thousands of people.
Followers in Nigeria and abroad believe he has the gifts of healing and prophecy.
Our correspondent says the coroner's verdict is really a recommendation and now it will now be up to Lagos state's director of public prosecutions to decide what legal action to take.
Profile: Nigerian preacher TB Joshua
In pictures: TB Joshua's ministry in 2005
A church run by the popular Nigerian evangelist TB Joshua should be prosecuted after the collapse of one of its buildings, a coroner has ruled.