NMC, which was founded by Shetty in the mid-1970s and has become the largest private healthcare provider in the UAE, was placed into administration this month.
Its shares, which NMC plans to delist in London, were suspended after more than halving in value since December, when short-seller Muddy Waters questioned its financial reporting.
The UAE freezing directive, which was issued by the central bank last week, extends to two other NMC shareholders, Khalifa al-Muhairi and Saeed Mohamed Butti Mohamed al-Qebaisi, the sources, who had seen the order, told Reuters.
The directive also calls for the freezing of bank accounts of several former executives including ex-CEO Prasanth Manghat and his family, two of sources said.
"Our businesses operate in areas such as food security and supply, pharmaceutical manufacturing, medical waste management and industrial catering services, and are therefore vital cogs in the economy," a spokesman for Shetty and his holding company BRS Ventures told Reuters.
"Any such orders would put these businesses, their employees and their ability to operate and meet ongoing supply at serious risk, and especially at such a critical time given the current public health issue," the spokesman added.
The UAE central bank did not immediately respond to a Reuters request for comment. Manghat, who has left the UAE, did not respond to a Reuters request for comment. A spokesman for Muhairi and Qebaisi had no immediate comment.
In recent months, NMC has revised its debt position to $6.6 billion (5.32 billion pounds), well above earlier estimates of $2.1 billion in June last year, after doubts emerged over the size of Shetty's stake and those of other shareholders.
Finablr, in which Shetty has a controlling stake, said last month it was preparing for potential insolvency, while operations of its UAE unit were seized by the central bank.
Shetty resigned as NMC's non-executive chairman and as a board member in February and has said he is conducting his own investigations.
By Saeed Azhar