They are some of the wealthiest people in Greece, the owners of the world's largest commercial fleet with bank accounts and property portfolios that, even by the standards of the super-rich, elicit awe. But in the high-risk business of trading the high seas, Greek ship-owners – in line with international maritime tradition – have also been granted special tax status on their vessels.

This week, the cash-strapped government in Athens insisted the preferential treatment – enshrined in the Greek constitution and respected by every government since the 1940s – was finally over. And shipowners are up in arms.

As it tries to steer Greece out of its worst recession on record, prime minister Antonis Samaras' fragile two-party coalition has suddenly found itself at war with the influential plutocrats who control one of the few thriving sectors of the Greek economy.

The imposition of extra taxes on the industry amounted to nothing less than a "constitutional deviation" warned Theodore Veniamis, the president of the Union of Greek Shipowners. "A negative climate has been created for any type of business investment in Greece," he said.

Samaras' conservative-dominated alliance rushed legislation through parliament, imposing a triple tax on ships managed out of Greece, as the 300-seat House held its last session before the Christmas break in December.

This week, the country's merchant marine minister said that the levy was an emergency measure that would last no longer than the next three years.

But while ordinary Greeks have been hit by a barrage of taxes since the debt-stricken nation was forced to accept international aid to avert bankruptcy, the country's famously secretive shipping community is digging in its heels.

The new tax law overturned a previous accord, signed after several months of talks last year, that had allowed ship-owners to make voluntary tax payments to help the nation's economic recovery. Most of the shipping companies run out of Athens' port of Piraeus – the industry's base in Greece – had agreed to back the voluntary scheme.

With unemployment at a record 28%, the highest in the European Union, and worsening social and economic marginalisation, the legislation has won praise. In its fourth year of bailout funds from the EU and International Monetary Fund, Greece faces fiscal shortfalls this year and next. Samaras has refused to take further unpopular spending cuts to plug the gap.

In a rare display of concord with the government, Giorgos Stathakis the shadow minister for development in the radical left main opposition Syriza party told the Guardian: "It's a positive step."

Yet the strength of reaction from shippers appears to have taken the Samaras administration aback. The industry, which provides up to 200,000 jobs and sustains close to 500,000, has warned that the new tax regime could force it to move elsewhere – potentially wreaking havoc on the economy.

"The fear is that the lack of trust between the maritime community and our legislators may lead to an exodus from the Greek flag and perhaps Greece itself," warned Haralambos Fafalios, who chairs the London-based Greek Shipping Co-operation Committee.

As a pillar of the Greek economy, shipping rivals tourism in attracting foreign exchange: experts estimate it has brought over ¤140bn (£115bn) into the country in the past decade alone.

"The shipping industry is a significant contributor to Greece in terms of jobs, cash and economic activity, and it stands to lose all three if it changes the regime for attracting shipping companies to the country," said Vassilis Antoniades, managing director of the Boston Consulting Group, which recently conducted an in-depth study into the impact of shipping on the Greek economy. "To a great degree the Greek economy thrives on the shipping industry."

Since the 1960s, shipping tycoons, such as Aristotle Onassis (pictured), have established airlines, shipyards, refineries and hotels in Greece. Indicative of their pre-eminent role in a sector now worth about $660bn (£400bn), this year Greek shipowners placed a record number of orders to build new vessels in shipyards around the world, outstripping any of their global competitors.

With earnings from shipping accounting for around 7% of GDP, fears are growing that the government's step could ultimately be counter-productive – even if, in poverty-stricken Greece, many also accept that may also seem rampantly unfair.

"There are alternatives with other countries offering competitive tax regimes. People will simply register their ships elsewhere," said shipping expert David Glass, who said that the sector had been unfairly reviled. "Shipowners give a lot to this country. They've built half the hospitals on the islands. They're the ones building schools and handing out over 50,000 meals to the needy every month. People forget that."