70-year-old Olmert entered Ma'asiyahu Prison in Ramle this morning, nearly two months after the apex court upheld his bribery conviction.
Earlier in the morning, hours ahead of his incarceration, he insisted that while he accepted the sentence, he was innocent of taking bribes, the Times of Israel reported.
"As prime minister I was entrusted with Israel's security, and now I am the one who is about to sit behind bars. You may well imagine how this transformation is painful and strange to me," Olmert said in a short video released shortly before he departed for the prison.
"It is also important for me to note that all the charges do not touch on the time of my tenure as prime minister. It is with a very heavy heart that I accept the sentence - no one is above the law," he concluded.
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A Jerusalem court last week added another month behind bars to his jail term after he pleaded guilty to obstruction of justice in various cases against him.
The plea deal was the first admission of wrongdoing by the former premier and Jerusalem mayor, who has consistently maintained his innocence throughout eight years of legal proceedings in various graft cases.
In December, the Supreme Court reduced Olmert's sentence from six years to 18 months in prison, and acquitted him on one of the charges, bringing an end to what was dubbed the largest bribery scandal in Israel's history.
The Holyland scandal refers to a housing project of high rise buildings over a hilltop overlooking the city.
In 2010, Olmert was named the key suspect in the case and was accused of receiving hundreds of thousands of shekels for helping developers get the project past various legal and planning obstacles.
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A total of 13 government officials, developers and other businesspersons were charged in three separate graft cases linked to the scandal.
Among those convicted included former Jerusalem mayor Uri Lupolianski and Danny Dankner, former chairman of Bank Hapoalim, Israel's second-biggest bank.
Olmert expressed regret that his term as prime minister concluded under the shadow of a police investigation.
"This is an unusual and grave development, which some will see as confirmation of the Israeli democracy's might. But in the same breath I would like to raise the possibility that the legal case against me snowballed due to non-judicial reasons. Perhaps once time passes the public could examine this sad moment through critical and balanced eyes," he said.
The former premier also rejected charges of bribery saying "I made mistakes, but they were not criminal in nature".
Olmert had to go through the same procedure as every prisoner when he entered the prison and was allowed to bring with him the same clothing and personal effects as other prisoners - four pairs of underwear, four pairs of socks, two towels, two tracksuits, a single-sized blanket and cover, two bedsheets, a pillow case and personal hygiene products.