The head of one of the world's largest bitcoin exchanges told CNBC that the ban on the virtual currency by Chinese e-commerce giant Alibaba won't affect his business.

Chinese e-commerce group Alibaba said Tuesday it would note accept bitcoins on its online marketplace, Taobao. It also banned the sale of the equipment, merchandise and software used to mine the virtual currency.

"We've found other methods to allow our customers to deposit money into our exchanges to buy and sell bitcoins so our business is unaffected by the recent Taobao decision today," Bobby Lee, chief executive of bitcoin exchange BTC China, told CNBC.

Alibaba's actions are seen as a response to the People's Bank of China (PBoC) warning against the use of Bitcoin last month as it looks to IPO this year and attempts to rid its marketplace site of fake goods.

In mid-December, the price of bitcoin plummeted by 50 percent since record highs of $1,200 in late November after reports that the PBoC had ordered third-party payment providers -- which provide clearing services for bitcoin exchanges -- to stop any "custody, trading and other services" related to the virtual currency.

(Read more: Bitcoin price halves as China clampdown escalates).

At the moment the the currency was trading at $920 on major exchange Mt Gox and $856 on CoinDesk's index, which measures a basket of prices around the world.