The three are also accused of defying a summons to appear in court last month.Pfizer is accused of killing 11 children and injuring 181 others when an antibiotic called Trovan was tested on them during a meningitis epidemic.
But Pfizer denies the claims, saying they were victims of the outbreak which killed 12,000 children in six months.
The northern state of Kano is suing Pfizer for $2bn in damages and pressing criminal charges over the test.
But the company, as well as denying any wrongdoing, has challenged the jurisdiction of the Kano state court.
Presiding judge Shehu Atiku said the three accused, all residents in Nigeria, had been served summonses to appear before the court on 6 November.
"But up till this moment none of them has appeared before this court either out of neglect, disrespect or contempt," the judge said before issuing the arrest warrant.
"There is no information on why they have refused to comply with this court's order," he added.
The case has been adjourned until 29 January 2008.
© 2007 BBC News