The railway is the only coal export route for mining giants Vale and Rio Tinto, and its closure has severely impacted both companies.
Vale declared a force majeure on February 15, failing to deliver 250,000 tonnes of coal to Beira for export.
Rio Tinto has suspended all activity at its open cast mine in Benga until rail services resume.
"We have sent a letter to the coal exporters last week that the line is open although they have yet to start sending trains," director of the Sena railway rehabilitation project Sancho Junior said.
Heavy rain and flooding since early February affected about 8km of the line, costing Mozambique’s port and rail company, CFM, about $8 million in lost business.
Mozambique transport minister Paulo Zucula told allafrica.com that the rain was not the only problem with the rail.
He alleged that work done by Indian contractor Rites and Ircon International (RICON) in rebuilding the Sena line was not up to standard.
CFM and the government have previously criticized RICON for lengthy delays and poor workmanship.
Zucula said the rail damage was not merely due to the rains.
“It is the result of the line that we built,” he said.
“You know we had a long history with RICON in which we said they were building the line badly. This is further proof that the drainage system they installed was of the wrong size”
The minister believes when its problems with RICON began and the government threatened to rescind its contract, the Indian consortium cut corners in an attempt to finish the job.
“They concluded the work badly and we are suffering for this,” he said.
“This damage did not happen because of lack of planning, lack of engineering, much less lack of knowledge. The line was badly built”
CFM is working with Portuguese building company Mota-Engil to complete an upgrade of the line.