Abd al-Jabbar van de Ven, a Dutch convert to Islam, told a Dutch television chat show on Tuesday he hoped anti-immigration populist Geert Wilders will soon die of natural causes.
Interior Minister Johan Remkes said he was horrified by the remarks and said the Justice Ministry will look into the matter. "It is too crazy for words," he told Dutch news agency ANP.
Immigration Minister Rita Verdonk agreed. "How can it be that we have sunk so far in the Netherlands? I am really worried about this," she told Dutch television.
Wilders, whose popularity has soared since he called for a crackdown on Muslim "militants" following the murder of filmmaker Theo van Gogh this month, has been the subject of several death threats for his views on Islam and immigration.
Wilders is seen as a new Pim Fortuyn, the Dutch political maverick killed by an animal-rights activist in 2002.
Wilders wants to launch a new right-wing party ahead of elections due in 2007 and a recent poll put him ahead of the ruling Christian Democrats.
Van de Ven said he would prefer Wilders to die of an illness, like cancer, and added he had felt some happiness when he heard of the death of Van Gogh.
Theo van Gogh's murder has led
to an upsurge in Islamophobia
A Dutch-Moroccan man has been charged with murder and with threatening another politician.
In a declaration on Wednesday, Van de Ven - who converted to Islam aged 14 and is now a Muslim teacher with links to a Saudi foundation - said he had gone into hiding and had not wanted to urge anybody to kill Wilders.
Meanwhile, a debate raged in the Netherlands about Muslim treatment of women after an imam refused to shake hands with Immigration Minister Verdonk.
Imam Ahmad Salam told a news conference on Tuesday he was keen to talk to the minister about integration but said Islam prohibited contact with women outside the immediate family.
"It seems as if integration for Minister Verdonk is something that should lead to people outside of Islam saying how Muslims should practise Islam," he said.
The Netherlands, which is home to almost one million Muslims or about 6% of the population, saw a wave of apparent tit-for-tat attacks on mosques, churches and religious schools after the Van Gogh murder.