After independence, the Marxist Frelimo government nationalised the industry, creating a state operator called Navique. The 1980s civil war with rebel movement Renamo unleashed mass killings, starvation and economic devastation but for the cabotage industry, these were actually boom years. Up to 20 vessels were ferrying passengers and cargo up and down the coast.
"It was cheap and safe," recalls Bento Magno, who travelled from Inhambane province to Maputo in the 1980s. The trip took two days and a night and went smoothly, apart from crossing the Limpopo river mouth, where "we bounded around a bit".
With Renamo guerrillas controlling swathes of the country and carrying out ambushes on the roads, sea travel was the only way for Magno to reach Maputo to study. In many ways cabotage helped keep going what little commerce existed.
As one of the privatisations encouraged by foreign donors after the war, the state cabotage service ended up in the hands of a Portuguese company, Empresa da Trafego e Estiva. When the firm stopped offering the service in 2006, cabotage was mothballed.
Close to a decade later, it may be making a comeback. This is due as much to the resurgence of the Frelimo-Renamo conflict that has been simmering since the end of the Cold War, as to new natural gas discoveries.
So far, 170-trillion cubic feet of gas have been discovered. Most of that lies beneath the deep waters of the northern Rovuma basin near the border with Tanzania. The basin extends 160km out to sea and to just north of Pemba.
Oil majors Anadarko and ENI have yet to agree on production terms with the Mozambican government to build gigantic gas-to-liquids facilities.
In the meantime, suppliers and subcontractors have wasted no time in setting up operations in remote coastal terrain more suited to beach holidays than major extractive operations.
Getting to Pemba is a three-day road trip at the best of times. During the long rainy season from October to April dirt roads become mud-traps for trucks and swollen rivers cause flooding, making the roads impassable.
"If a bridge goes down we are completely lost. We can’t do anything," says Diogo da Cunha whose company, African Century, is setting up in Pemba and Palma to provide real estate and related services to the industry.
Using cabotage to get machinery and even food into remote places seems a no-brainer.
A German-Mozambican company, Rhenustora, so far is the only company licensed to run cabotage services. It began to ply between Maputo and Pemba in July last year with stop-offs in the central port of Beira, in Quelimane in Zambezia province and in Nacala in northern Nampula, a growing commercial hub where Brazilian company Vale is also developing a coal terminal.
Their 90m "coasters" are easier to land in smaller ports and inlets than larger cargo ships.
"All we need is a jetty and a crane," Rhenustora GM Armando Moreira told Business Day.
Some of the remote beaches where gas infrastructure needs to go do not have even these basics. Texas-based Anadarko is experimenting with using a "D-Day" style landing craft with a front ramp to deliver goods straight onto beaches.
The north is set for a boom in port infrastructure. The government recently awarded a concession to an Italian-Nigerian company, Orlean Invest, to build and operate ports dedicated to the gas industry in Pemba and Palma.
These projects will not be completed for at least another five years. In the meantime, cabotage represents an essential stop-gap. "If we can mitigate risks in the rainy season we would definitely use it," says Mr da Cunha.
Another risk that companies now have to mitigate is the renewed threat of conflict. On and off for the past 18 months Renamo gunmen have been ambushing cars travelling along a 100km stretch of the national highway just north of the Save River (the unofficial halfway mark). Though highly localised, this threat has been enough to paralyse transport at times. Scores of civilians have died. Vehicles have to travel in convoy guarded by the military, a process that can add as much as a day to the journey.
No new shootings have occurred along the Muxungue-Save stretch over the past two weeks after Renamo’s leader Afonso Dhlakama, declared an unofficial ceasefire. Dhlakama evidently hopes to sweeten negotiations with the government under way in Maputo and says he wants to be able to come out of hiding and campaign for presidential polls.
Although initially unwilling to consider using the sea because they had invested heavily in trucking over the past two decades, companies are now more interested in the option.
"Lately they are approaching us again because of the shooting," says Mr Moreira.
With so many reasons to choose the sea over road, why has the cabotage industry been so slow to take off?
"There are a few things not making our business as viable as it could be," says Mr Moreira.
Part of the problem is that the company can ship cargo from Maputo to Pemba in four-and-a-half days (it takes roughly four days by truck), but transporting cargo to the ship, loading it, and customs paperwork make it a 10-day trip door to door.
And, while the cost per tonne is half of what it costs to send cargo by truck, once the costs charged by individual port operators are considered, cabotage is not cheap enough to justify the extra time.