Mr Justice Weir described the situation as unacceptable after being told experts refuse to accept any more police exhibits after reaching their monthly quotas.
In a hard-hitting assessment of delays in some criminal cases, he suggested that the Justice Minister David Ford may have to "look closer to home" in efforts to speed up the system.
Unfavourable comparisons were made with the time taken to deal with high-profile murder trials in England and Wales. He also called for a media investigation to ensure the Stormont Assembly is fully aware of the funding.
"The idea that the forensic laboratory barricades its door in the middle of the month because it's done all the work it's paid to do is absolutely unacceptable," he said.
"It's about (time) the press carried out some sort of investigation into this and wrote some article about it.
"I don't think the public have any idea the fact that work is undertaken on a shoestring.
"Do members of the Assembly know? Does the Justice Committee know? Do any of these people know about what the situation is?"
The judge issued his comments after learning that test results on a suspected £150,000 batch of cocaine seized at the start of August will not be confirmed until mid-January.
He identified the prosecutions brought over murders of Drummer Lee Rigby and schoolgirl April Jones to make his point.
"The attack upon the off-duty soldier in England, or the case in Wales about the child that disappeared," Mr Justice Weir said.
"These cases from the date of commission to the date of trial are often dealt with in less than a year.
"Meanwhile, six months after the seizing of this material we are waiting to get information on whether it is or isn't cocaine."
One of the men allegedly linked to the find of three kilos of suspected cocaine at a house in Crossgar, Co Down is lorry driver John Harvey.
The 48-year-old, of Ardoyne Road, Belfast, faces charges of possessing, supplying and conspiracy to supply Class A drugs.
His legal team mounted a fresh High Court bail application, citing delays in the case.
A prosecution barrister said Forensic Science Northern Ireland refused to take the cocaine exhibit from police in August because it had already reached its target for the month.
It was then submitted at the start of September.
"They are described as being flat out in relation to their workload on drugs submissions," the prosecution lawyer said.
He was asked by Mr Justice Weir if the situation did not suggest more staff were needed.
"You can't just pile people up in prison while the Department looks for money to pay for forensic services to take drugs in to analyse them," the judge insisted.
During the hearing he also commented: "The Minister talks about fast-tracking justice... Well I think he might look closer to home."
He added: "Presumably it's a question of finance if forensic people are saying they have now done the work they are obliged to do under contract with the Department of Justice.
"That means the Department of Justice have not funded the forensic laboratory to enable this work to be done."
Despite expressing sympathy for the situation of police in the case, the judge stressed that he was dealing with a man being held in custody.
Adjourning the application to 20 January for the forensic results to be confirmed, Mr Justice Weir concluded: "We really have to get a system going in this country where materials required to be examined are properly examined."