Incheon Metropolitan Police chief Kim Hui-jung told a news briefing the entire process was justified and done with Lee's consent. He expressed "deep regret" over his death and offered his condolences to his family.
Lee, 48, who played the wealthy patriarch in the Oscar-winning film "Parasite", died on Wednesday.
His death brought an outpouring of sympathy from the film industry and the public alike as well as questions over the apparently harsh and public nature of the probe that fuelled media coverage delving into Lee's private life.
Kim said the questioning over Lee's three appearances, including a final one that went on all night, was necessary to hear his side and was done in the presence of his lawyer.
"The investigation of the deceased was conducted based on specific reports, testimony and evidence and under legally prescribed procedures," he said.
Lee had denied he knowingly took illegal drugs and said he was tricked into doing so by a bar hostess who was trying to blackmail him, local news media reported before his death.
He made three highly public appearances before police since October, the last time for 19 hours overnight, leaving the police station on Christmas Eve.
He declined to answer questions from reporters about the charges against him but said he was fully cooperating with the investigation.
He was found dead in a car at a park in Seoul after being reported missing.
Former South Korean President Moon Jae-in, who was a human rights lawyer before entering politics, was among those who criticised police practice and sensational media reporting of the case.
"The practice that does huge damage to someone's honour and character, such as excessively putting them at a media photoline, and pushes them to take the extreme choice must now end," Moon said on Facebook.
Film industry colleagues visited the memorial set up at Lee's wake, including "Parasite" director Bong Joon-ho and the Netflix hit series "Squid Game" actor Lee Jung-jae.
Incheon police had earlier questioned K-pop star G-Dragon over suspicion of illegal drug use but dropped the case without charging him.
The probe comes as part of a crackdown by the government of conservative President Yoon Suk Yeol, who called it a "war on drugs".
There has been a string of high-profile arrests, including business conglomerate heirs and celebrities, under the country's tough drug laws, which punishes those found guilty of abusing drugs as well as drug dealing by up to 14 years in prison.
(Reporting by Jack Kim; Editing by Angus MacSwan)
By Jack Kim and Jimin Jung
