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Judge Paul - who had sole discretion in deciding whether he should stand down - ruled that it would be "wrong in law" for him to be replaced.
He said that although certain rulings may put a particular party at a disadvantage, it was contemptuous to say those rulings had prejudiced the defendant.
Judge Paul told the defence that the correct way to challenge his rulings was at the court of appeal.
Application opposed
The prosecution in Mr Anwar's trial had opposed the application for the judge to stand down.
Mohtar Abdullah, Malaysia's Attorney General and chief proescutor in Mr Anwar's trial, said the defence team had acted with bad intent for filing their application to remove Judge Paul so close to the end of the trial
The former deputy prime minister is being tried for corruption, accused of abusing his office to try and cover up allegations of sexual misconduct.
![[ image: width=150]](/olmedia/295000/images/_296955_judgepaul150.jpg)
He still faces separate charges of sodomy.
Mr Anwar has maintained his innocence since he was arrested in September, saying the charges are part of a conspiracy by his political opponents in the government.
Prime Minister Mahathir Mohamad had dismissed Mr Anwar from his position as deputy shortly before he was arrested.
Earlier this week, the defence refused to make their closing arguments until their application for the judge to step down had been heard.
Judge Paul responded by citing Mr Anwar's legal team for contempt of court.
The verdict is due on 6 April.
Abrupt end for Anwar trial
(23 Mar 99 | Asia-Pacific)
Taking stock of the Anwar trial
(11 Feb 99 | Malaysia crisis)
Anwar: The re-written charges
(13 Jan 99 | Malaysia crisis)
The case against Anwar
(05 Oct 98 | Malaysia crisis)
Prime Minister's Office of Malaysia
Anwar Online
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