The order comes as political tensions remain high on the deeply divided island after the Beijing-friendly KMT were ousted by a landslide in January elections.
The new Beijing-sceptic Democratic Progressive Party government announced a probe into the assets of all parties in late July, but it is only the KMT that has faced questions.
The KMT is thought to be one of the richest political parties in the world and registered total assets of Tw$18.96 billion (USD 600 million) by the end of last year, compared with Tw$478.72 million by the DPP.
It also inherited assets nationalised by the Japanese, who ruled Taiwan as a colony from 1895-1945.
However, critics have long accused the party of stealing from the people of Taiwan and illegally amassing fortunes through cosy business links during its half-century grip on power.
Government investigators say the KMT withdrew Tw$520 million (USD 16.6 million) from Taiwan's Bank SinoPac soon after the asset probe got under way and exchanged it for 10 cashier's cheques from the state-run Bank of Taiwan.
KMT officials say it was used to pay salaries and pensions.
But investigators say the money should not have been moved since the probe had already started.
The party has slammed the investigation as a witch-hunt.
"The KMT violated the law which prohibits it from moving its assets," the Ill-gotten Party Assets Settlement Committee said in a statement.
"Bank SinoPac has been notified to halt withdrawing or transferring money from that account."
The freeze was the asset committee's first major action against the KMT.
KMT chairwoman Hung Hsiu-chu called it a "vendetta" and said the party should rally outside president Tsai's home.
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