Rather than a cyberattack, the security issue was in the real world, with Mt Gox saying it had to relocate to another part of the capital.
"In addition to the technical issue, this week we have experienced some security problems, and as a result we had to relocate Mt Gox to our previous of¿ce building in Shibuya," it said.
"The move, combined with some other security and technical challenges, pushed back our progress...we are committed to solving this issue and will provide more information as soon as possible."
Mt Gox customers have been unable to withdraw their bitcoins and convert them into US dollars since the beginning of February. The bitcoin exchange then blamed the problem on a critical flaw in the cryptocurrency - known as "transaction malleability" -- which it said affected all exchanges.
On Monday, the exchange announced that users should soon be able to withdraw funds from their accounts amid growing tensions and a price collapse for the virtual currency. However, Thursday's update revealed that users still won't be able to able to transfer their investments.
(Read More: Bitcoin exchange to resume withdrawals after slump )
The price of the virtual currency plunged to below $200 on the exchange Thursday, compared to a figure of around $600 on other major exchanges. Bitcoin had traded above $1,200 at its peak back in November but has since halved in price.
The Mt Gox breakdown has caused anger in the bitcoin community with customers taking to social media to express their dissatisfaction amid rumors that the company could be concealing financial difficulties.
Ezra Galston, a venture capitalist at Chicago Ventures, wrote in an editorial on the bitcoin community news website CoinDesk this week, saying he believed that the current situation and recent statements belie transparency and suggest insolvency for Mt Gox.
Meanwhile, the Wall Street Journal asked Mt Gox chief executive Mark Karpeles on Monday about the company's solvency or protection for customers' funds. Karpeles replied that the matter is "confidential" adding that company had discussed its business model with Japanese authorities "to ensure that we are operating within the law here."
The Japanese company - which started as an online exchange for Magic The Gathering trading cards - has been described as the "original" bitcoin exchange by fans of the digital currency and once it handled around 80 percent of all global dollar trades for the currency.
It is currently the second-biggest bitcoin exchange in the world - representing around 25 percent of total bitcoin trade in the last week, according to Bitcoinity.org.
A small protest outside the offices of Mt Gox has been ongoing since last Friday. Two Mt Gox customers, including former software developer Kolin Burges, have traveled to Japan in the hope of retrieving their bitcoins and finding out more details of the trading halt.
Burges told CNBC via telephone that there had been implications that the protest has been the reason for Mt Gox's move, with an angry landlord threatening to expel the company. However, Burges said he didn't believe this to be the case and considered that the company may have been the subject of a more formal physical threat from users with large deposits at Mt Gox.
"Nobody is really sure of what is going on," he said. "I have seen a couple of large security guards at the offices all day today."
Mt Gox wasn't immediately available for comment when contacted by CNBC via telephone and email.
The current three-person protest is expected to grow on Friday with the bitcoin community meeting in a Tokyo bar on Thursday evening amid increasing concerns about the future of Mt Gox.
(Read More: Bitcoin drops another 20% as Mt Gox highlights bug )
This is not the first public relations problem Mt Gox has run into.
It recently experienced lengthy delays when exchanging bitcoin into U.S. dollars and has previously experienced high-profile DDoS (distributed denial-of-service attacks) hacking attacks which slowed the site down. Meanwhile, the U.S. Department of Homeland Security seized its bank account in May 2013, saying it had never properly registered as a money services company.
-By CNBC.com's Matt Clinch; Follow him on Twitter @mattclinch81
image: © Zach Copley