An Israeli court on Tuesday sentenced the former Gaza head of a major US-based aid agency to 12 years in prison for funnelling millions of dollars to Islamist group Hamas.

The Beersheba district court in southern Israel issued a sentence of "12 years prison time, less the detention" already served for World Vision's Mohammed al-Halabi, who has been jailed throughout the past six years of court proceedings.

The sentencing comes after the court issued a ruling in June that Halabi was guilty of siphoning off millions of dollars and tonnes of steel to Hamas, which controls the Palestinian enclave.

Halabi, who was arrested in June 2016 and indicted in August that year, has consistently denied any irregularities.

His lawyer reiterated his claim to innocence following Tuesday's sentencing.

"He says that he's innocent, he did nothing and there is no evidence," Maher Hanna said. "In the contrary, he proved in the court above any reasonable doubt that he made sure that no money will be (given) directly to Hamas."

Hanna said they would appeal the verdict to the supreme court.

Halabi had been convicted of membership in a terrorist group -- Hamas -- and of financing terrorist activities, of having "transmitted information to the enemy" as well as the possession of a weapon.

Much of the evidence against Halabi was kept secret, with Israel citing "security concerns", prompting his legal team to question the verdict's legitimacy.

Following Halabi's arrest, the Australian government, a major donor to World Vision, announced it was freezing funding to projects in the Gaza Strip.

A subsequent Australian government probe found no evidence of embezzlement.

World Vision is a US-based Christian charity with almost 40,000 employees globally.

It claims to be one of the largest non-governmental organisations in the world, with a particular focus on children.