But Justice Mark Woolford said there was no evidence of prosecutorial misconduct in the delays and the submissions did not meet the high threshold for a permanent stay of proceedings.
The trial, in which Karpavicius is charged with importing Class A and B drugs as well as money laundering, is scheduled for September and will go ahead.
He has pleaded not guilty.
The 33-year-old was living overseas but his name surfaced at a trial in the High Court at Auckland in 2010 where he was alleged to be the head of a global drug and money-laundering syndicate.
The Operation Keyboard investigation began in Australia in January 2008 when Sydney police discovered that a shipment of granite sculptures sent from Lithuania concealed 28kg of amphetamine.
Further inquiries found a nearly identical shipment to Sydney in February 2007 and two to New Zealand that same year.
The police case is that Karpavicius was the man behind the drug smuggling enterprise and his prints were allegedly found on a Harry Potter book couriered from Spain to Auckland which had the Class A drug LSD hidden in its spine.
Photographs produced at the original trial show Karpavicius lounging on a luxury yacht in Europe surrounded by bikini-clad women.
He was arrested in Latvia in late 2011 where he was held in custody and two detectives escorted him back to New Zealand last October.
Rokas Karpavicius
*Born in Lithuania
*2010: Identified in a High Court trial for Operation Keyboard as the alleged mastermind smuggling drugs into New Zealand.
*2011: Arrested in Latvia on an Interpol warrant.
*2012: Extradited to New Zealand to face Operation Keyboard charges.
*2013: Due to stand trial on charges of importing Class A and B drugs as well as money laundering.