The digital currency hit a low of $6,307.31, breaking below $6,400 for the first time in about a week.
The order led bitFlyer — the largest crypto exchange in Japan — to suspend the creation of new accounts while it makes improvements to its business.
The agency gave the same order to five other other exchanges after finding weaknesses in their money laundering controls.
Bitcoin prices fell more than 5 percent on Friday after Japan's financial regulator ordered several cryptocurrency exchanges to improve their practices against money laundering.
The digital currency traded at $6,349 as of 7:45 a.m. ET, breaking below $6,400 for the first time in about a week, according to CoinDesk.
The order from Japan's Financial Services Agency led bitFlyer — the largest crypto exchange in the country— to suspend the creation of new accounts while it makes improvements to its business, especially in its measures to stop money laundering and terrorist financing.
"Our management and all employees are united in our understanding of how serious these issues are, as well as how serious we are in responding to them going forward," bitFlyer said in a statement on their website.