Mr Ahmed said three employees of the company had been arrested and on the basis of disclosures made by them an investigation had been launched against a number of customs officials and a case had been lodged.

Over the past 27 months, 14,000 containers with goods for Isaf in Afghanistan had been allowed transit by the Model Customs Collectorate at Port Qasim and Karachi port, he said.

In one of the containers, a large quantity of liquor was found which was to be sold in Pakistan.

FBR Member (Customs) Munir Qureshi said “our people” were also involved and an investigation was under way on the basis of intelligence reports.

The board's chairman said all goods imported by Nato were exempted from inspection under the Customs General Order (CGO).

It is the responsibility of the National Logistics Cell (NLC) to ensure their secured transit up to the Afghan border. The NLC uses hired mechanical transport.

“We are going to re-draft the CGO,” Mr Qureshi said, adding that the matter had been discussed at a meeting attended by officials of the ministries of defence, finance and the departments concerned.

A statement issued by the FBR said that after detecting the case it lodged an FIR two months ago regarding a container belonging to the Luner Products which had been seized at the Karachi port before clearance.

Parvaiz Ishfaq Rana adds from Karachi The FBR has sought a detailed report from the director-general of intelligence and investigation on alleged misuse of the facility and clearance of contraband goods.

The investigation has been in progress for over a month and the I&I directorate-general in Peshawar has issued arrest warrants for some customs officers and agents.

In a letter to the director-general of intelligence and investigation headquarters, the FBR sought an interim report on the seizure of liquor in Isaf cargo and detailed break-up of 11,000 un-reconciled containers cleared in Karachi.

However, official figures of containerised imports of Isaf cleared by the Model Customs Collectorate and MCC appraisement between Jan 1, 2008, and March 31 this year tell a different story.

According to the figures, 11,167 containers with import value of Rs23.16 billion were cleared by both the collectorates. The director-general for intelligence and investigation has put almost the entire quantity under suspicion of contraband goods having been cleared.

According to customs sources, it means that only 167 containers cleared over more than two years belonged to Nato and the remaining 11,000 fell under misuse of the facility.

The clearance of Nato transit cargo for Afghanistan is governed by special notifications issued by the commerce ministry and the CGO which allow import of banned items like liquor and pork exclusively for Isaf personnel.

To ensure that the facility is not misused, the Afghan government has to certify each consignment that has to be transported by bonded vehicles.

Customs sources told Dawn that the Peshawar I&I DG had recently seized a container (GD-AT No.KAPR-AT-32478) with a declaration of assorted beverages. On investigation it was found that the container did not belong to Isaf and this was also confirmed by the force's headquarters in Kabul.

A joint inspection by intelligence and customs personnel revealed that the container carried liquor and other contraband items.

However, a letter by the Afghan consulate-general in Karachi certified that the container (GD-AT) was meant for Isaf, the sources said.

The sources said that under the cover of Nato supplies a large number of containers carrying contraband goods, including arms and ammunition, liquor and other high-value items, were cleared and found their way into the local market.

After the seizure, Peshawar I&I DG issued arrest warrants of some customs officers for not appearing before an investigation team.

The move created tension at Karachi customs and the Pakistan Appraisement Officers' Association went on strike last week which was called off two days later on the intervention of Chief Collector (South) Sher Nawaz.

Mr Nawaz assured the officers that no arrest would be made till June 30 and asked them to concentrate on revenue collection ahead of the fiscal close.

During the strike, movement of containers and cargo from ports and the Air Freight Unit (AFU) came to a halt and no collection of duty and taxes was made.The chief collector said the FBR would never back those who had violated the law or were part of the scam and the investigation team would be allowed access to the entire record.

He said the team had already recorded statements of some officers and all matters would be sorted out in accordance with the law. Therefore, the officers involved in the matter may have to seek bail before arrest.