Abdullah Badawi said there was nothing to fear from the truth.
Police say foreign intelligence warned them that Malaysian centrifuge parts were on a Libyan-bound ship last year.
The company, controlled by Kamaluddin Abdullah, made the parts after being told they were for oil and gas work, a spokesman said.
"We received the drawing for the part and made it according to the drawing. We were told these parts were for the oil and gas industry," factory manager Che Lokman Che Omar told reporters.
The BBC's correspondent in Kuala Lumpur, Jonathan Kent, says that the Malaysian media have been slow to draw attention to the links between Scomi and the prime minister's son.
The Malaysian government has denied that the country in any way contributed to the spread of nuclear technology.
"Investigations so far showed that not one company in Malaysia has the ability to manufacture a complete centrifuge unit," Malaysia's Inspector General of Police Mohammad Bakri Omar said in a statement.
"This requires technological capability and high expertise in the field of nuclear weapons," Mr Bakri said.
Analysts say the news of Scomi Precision Engineering's involvement in the probe could be embarrassing to Mr Badawi, who was only appointed prime minister last October.
Mr Bakri said the tip-off was received by British and US intelligence services in early November.
He said the CIA and MI6 claimed the parts had been found a month earlier on board a ship heading to Libya during a stopover in Italy.
"The components were said to have been placed in wooden boxes labelled Scomi Precision Engineering Sdn Bhd (Scope). Scope is a subsidiary of Scomi Group Bhd," said a police statement.
Scomi - a medium-sized oil and gas company - said Scope had been awarded a contract to provide tooling services to a Dubai-based firm.
In a statement, the company said it shipped the components in four consignments to Dubai between December 2002 and August 2003.
Scomi said the contract had been arranged by BSA Tahir, a Sri Lankan businessman who is currently under investigation in Malaysia. They were not told the "end-use" of the components.
"The company was recently informed by the Malaysian police that Mr Tahir is currently the subject of an investigation by Malaysian, American and British intelligence authorities over his alleged involvement in the supply of nuclear technology to Libya," said Scomi.
A high-level government source noted that any firm knowingly involved in the clandestine nuclear trade was unlikely to label its cargo with its own name.
Mr Bakri said Mr Tahir was co-operating in the investigation and was not under arrest.