The owner of a maraschino cherry company shot himself dead on Tuesday as police broke into a secret drug lab hidden behind the factory walls.

Company president Arthur Mondella, 57, had cooperated with investigators for five hours who were at Dell's Maraschino Cherries factory in Brooklyn, New York over allegations the generations-old, family business had been dumping hazardous waste.

Investigators reportedly came across suspicious shelving in a storage unit - then behind a door found a false wall with the smell of weed seeping through.

The entrance to a dug-out basement was then found, with three bags of marijuana inside.

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Arthur Mondella, (pictured) 57, the owner of Dell's Maraschino Cherries, shot himself in his office bathroom at the company's factory in Brooklyn

FBI crime scene investigators leave the maraschino cherry factory in Brooklyn with bags of evidence on Tuesday

A pot operation was found to be operating behind the walls of the family business during a separate investigation into hazardous waste

The factory floor at Dell's Maraschino Cherries - behind the owner's office, shelves of pot and hundreds of thousands of dollars was discovered

According to the NY Post, generators were found inside the factory along with a high-tech security outfit of dozens of cameras, barbed wire and motion-detector lights.

Mondella then excused himself to go to his private bathroom, locked the door and shot himself at 1.30pm, a law enforcement source told Daily Mail Online.

Before committing suicide, the third-generation cherry tycoon told his sister who was present, Joanne Capece, to 'take care of my kids'.

Those present heard a single gunshot, according to CBS New York. Mondella later died at a local hospital from the .357 magnum gunshot wound.

Family man: Arthur Mondella with his daughters Dana Mondella Bentz (left), Dominque Mondella (center) and wife, Elaine Pajchert Mondella pictured for for Dominque's 16th birthday

Arthur Mondella asked his sister Joanne Capece (pictured left) to 'take care of his kids' before taking his own life at his factory on Tuesday. His daughter, Dominque Mondella, who promoted the business in the press late last year (pictured right with boyfriend Michael Palmieri)

Salvatore Capece (left), nephew of owner Arthur Mondella, and Dominique Mondella, his daughter, continue family legacy at Dell's Maraschino Cherries Company (pictured in 2009)

Dominque pulls a cherry from the vat at the family business at Dell's Maraschino Cherries factory in Brooklyn

Mondella had a gun permit but it was unclear if he was carrying weapons at the time.

Daily Mail Online was awaiting a comment from the Brooklyn District Attorney's office on Wednesday.

The DA's office and environmental regulators discovered 80lbs of pot in three large bags and hundreds of thousands of dollars concealed in the secret room.

Shelves operated by magnets had been used to conceal the operation.

A row of luxury, vintage cars were also found covered in tarp in a back lot of the factory in the industrial area of Red Hook.

Calls to the business went unanswered on Wednesday.

Investigators had been looking into the company over allegations it was dumping hazardous material into the sewage system and waterways - but had suspected that the facility was also being used as a grow lab.

Hundreds of thousands of dollars along with 80lbs of marijuana were reportedly discovered in the secret room behind the factory walls in Brooklyn, New York

One official told the New York Daily News: 'It appears there was another activity going on, that's for sure. I don't think you kill yourself over a bag of weed. There has to be more to it.'

Brooklyn District Attorney's office had received a tip-off about the marijuana operation in 2013, the New York Post reported.

Despite watching comings and goings at the factory for six months, the DA's office was unable to work out if there was a marijuana business operating inside.

An anonymous source told the paper that the environmental offense warrants were simply used to get into the building.

The DA's office said 'no further information about this tragedy is available at this time'.

Officers consult paper work during the investigation of the cherry factory on Tuesday. The Brooklyn district attorney's office had a tip-off in 2013 that the firm was fronting a marijuana operation

The production line at the cherry factory (left) and a jar of Dell's Maraschinos from the company which has been in business for 76 years

The NYPD have become involved in the investigation and were seen removing bags of evidence from the factory late on Tuesday.

Dell's Maraschino Cherries, which has been in business for 76 years, supplies to Red Lobster, Buffalo Wild Wings, Chick-fil-A and TGI Fridays for use in cocktails and desserts.

Arthur Mondella's grandfather, Arthur Mondella Sr, started the business as a Brooklyn storefront in 1948.

The Brooklyn factory now turns out 400,000 bottles of cherries each week - and 19 million pounds of cherries a year.

The company recently underwent a $5million overhaul and redesigned their bottles with a retro label last year after the company suffered following the financial crash in 2008.

At the time Mr Mondella told The Wall Street Journal: 'At this point, the maraschino cherry is just another commodity. We’re trying to change that.'

Some 25 investigators arrived at the facility at 8am on Tuesday with search warrants to inspect its operations.

Mondella is survived by his ex-wife Yevgeniya and their five-year-old daughter Antoinette.