Anwar has said the meeting at Najib's home is proof he is the victim of a political conspiracy, but the prime minister has denied interfering in the case.
Saiful told the court that he met Najib on March 24, two days before his deposition stated that the 63-year-old opposition leader had sodomised him - a crime in Malaysia - and four days before he went to the police.
"I told him [Najib] about my problems," Saiful, now 25, told the court without elaborating on the first day of his cross-examination by Anwar's lawyers on Monday.
The trial opened briefly in February with explicit evidence from Saiful, but was suspended as the defence pursued a number of unsuccessful legal manoeuvres.
|Saiful says he met the prime minister four days before going to the police [EPA]
During his testimony, Saiful had said that Anwar propositioned him for sex shortly after he arrived at a Kuala Lumpur apartment on June 26, 2008 to deliver a document.
Prosecutors have said that two days after the alleged incident Saiful underwent a medical examination at a hospital and that DNA tests on samples taken from his body showed traces of Anwar's semen.
Defence lawyer Karpal asked Saiful on Monday how the evidence remained intact, asking whether he had washed before saying Friday prayers the following day, according to Muslim rites.
"I only washed a little, I did not wash my bottom part," Saiful replied, explaining that he did so because he was in an "emergency situation".
Karpal also raised questions about two medical reports which appeared to contradict Saiful's allegations, and duelled with the prosecution over access to its witness list which it has refused to provide, along with evidence including medical reports and closed-circuit television footage.
If convicted, Anwar could be jailed for 20 years, a sentence that would, in effect, end his political career.
Anwar spent six years in jail after being convicted of sodomy in 2000, adding to an earlier sentence for corruption, following his sacking as deputy prime minister at the height of the 1998 Asian financial crisis.
The earlier sodomy conviction was overturned on appeal, allowing him to contest a parliamentary seat after polls in 2008 that saw the government that has now ruled Malaysia for 52 years suffer its worst ever setback in national and state elections.