Members of the Brotherhood, one of the oldest and most influential Islamist groups in the Arab world, won one-fifth of the seats in the Egyptian parliament in elections in 2005.
The group, which advocates change through democratic means, had to run as independents because the government refuses to recognise the movement or let it form a political party.
"The accused have been receiving money from outside the country to finance the Brotherhood's wicked activities"
In its ruling, the Cairo criminal court dismissed the group's attempt to have the freeze overturned and appointed an official of state-run National Bank of Egypt to manage the assets.
It said the prosecution had given enough evidence that the accusations of money laundering were serious.
"The accused have been receiving money from outside the country to finance the brotherhood's wicked activities, buying and setting up commercial companies and investment institutions as a cover to hide the sources of these funds," the court said.
Authorities have given no estimate of the value of the assets.
A brotherhood official said on Wednesday that 186 members of the group remain in custody.