The line is the only available export route for mining giants Vale and Rio Tinto .
"No trains are running today. I don't know when the line will reopen," Nelson Semente said.
The temporary shutdown is a further blow to companies which are already battling with major infrastructure bottlenecks in the former Portuguese colony, home to vast reserves of coking coal, used in steel making.
Vale was forced to curtail its output and export targets last year and Rio Tinto wrote down $3 billion on its Mozambican assets, partially due to infrastructure constraints.
Other companies have had to delay their production plans, waiting until they can get their coal to port without having to use expensive trucks.
Vale and Rio Tinto officials were not immediately available for comment.
Semente said the Sena line was particularly prone to flooding on the first 100 km of the route and CFM was hoping to eventually elevate the tracks to avoid that, although he could not say when that would happen.
He said the company was working to increase capacity on the line to 6 million tons by the end of this year from around 2 million tons now and double that the following year, suggesting a further 12-month delay from estimates given by other officials towards the end of last year.
"The companies have found much more coal than we had expected so our greatest difficult is to keep up with the development," he said. "We just aren't able to."
The line should be able to carry around 18 million tons by 2015, he added.
Apart from the Sena line, Mozambique has plans for four new rail and port projects that together could raise the annual coal export capacity from Tete to more than 120 million tons, but it will likely take more than a decade to materialize. (Reuters)