DM Jayaratne DM Jayaratne said that that police investigations into the heroin seizure are continuing Sri Lanka's prime minister has ordered staff not to write letters in his name, after drug traffickers obtained a letter written by a secretary in his office to authorise a heroin shipment.
DM Jayaratne said that action would be taken against the sender.
At least 131kg (288lb) of heroin worth millions of dollars was seized on 30 August.
The heroin was hidden in cans packed into a container sent from the Pakistani port of Karachi.
It was concealed among ceramic bathroom fittings and plastic goods.
A customs official was quoted as saying it was the largest seizure of the drug in the South Asian region.
It had been unloaded at Colombo's port two months earlier and was addressed to a local recipient, but had been held pending production of documents and cash needed for its import.
'Not small-time'
A letter emerged from the prime minister's office, dated 23 August and signed by a co-ordinating secretary who said he would be "thankful on behalf of the Hon Prime Minister" if action was taken to waive import charges.
The letter said it was being imported by a local company which was just launching its business and could not afford heavy duties.
In his statement Mr Jayaratne acknowledged that a secretary in his office had sent the letter, saying "police investigations with regard to this are continuing".
It was not yet possible to say under whose instructions the letter was issued, he added, but parliament would be informed once the person was disciplined.
The statement said a Pakistani national and a Sri Lankan had been arrested in connection with the case.
Another Pakistani, said to be responsible for the smuggling, left Sri Lanka before the seizure but had now been taken into custody in his home country.
Three Pakistani anti-drugs officials are due to arrive in Sri Lanka to help investigate the case and Interpol assistance has also been sought.
The issue was raised in parliament by opposition MP Anura Dissanayake, who said the importers were clearly "not small-time smugglers".
"As in the case of many fraudulent businesses they, too, seem to have had the blessings of politicians," he said.
Media reports have highlighted the possibility that Sri Lanka is becoming a trans-shipment hub for narcotics.
BBC News, Colombo