A Croatian court on Monday sentenced former prime minister Ivo Sanader to six years in jail and the boss of Hungary's energy giant MOL to two years for bribery.

The long-running legal battle has been a thorn in relations between the two countries for years and harkens back to a 2009 deal that gave MOL control over the Croatian oil and gas group INA.

Sanader -- already serving time for a separate graft case -- and MOL's CEO Zsolt Hernadi were found guilty of "receiving and giving a bribe".

The deal was to give then-PM Sanader 10 million euros ($11 million) in exchange for boosting MOL's control over the Croatian energy group, said Judge Maja Stampar Stipic.

MOL, whose main shareholder is the Budapest government, has a 49 per cent INA stake, while Zagreb holds a 44 per cent stake.

"As the top state official, Sanader ... jeopardised Croatia's vital economic interests," prosecutor Tonci Petkovic said in his final statement.

Defence attorneys for CEO Hernadi, who was tried in absentia, argued that the prosecutors did not prove an "incriminating tie" between the two defendants, who can appeal the ruling.

"We are disappointed but not surprised: this is not the first unfair trial to be held in Croatia," MOL said in statement voicing continued to support Hernadi.

Croatia has unsuccessfully sought the CEO's arrest for years, with Hungary's refusal to extradite him a source of tension between the EU neighbours.

Sanader, whose lawyers said they planned an appeal, was first found guilty of the charge in 2012, but the country's top court overturned his eight-and-a-half-year jail sentence and called for a re-trial for procedural reasons.

Prime minister from 2003 to 2009 with the conservative HDZ party, Sanader has been trailed by scandals since he left office.

In April he was jailed to serve a six-year sentence in a separate corruption conviction for taking more than two million euros ($2.2 million) in kickbacks from a real estate deal.

In 2018 he was also sentenced to two and half years for war profiteering, and acquitted of abuse of power charges in another trial.

Sanader is the highest official to be charged with corruption in Croatia since independence from Yugoslavia in 1991.

Tackling corruption was key for the country's successful bid to join the European Union in 2013.