The SEC accuses "unknown traders" of having advance word of the deal and buying options a day ahead of the news to make "risky bets" that Heinz's stock price would rise. Both the size and the timing of the trades raised suspicions at the SEC.

According to the government, the traders made more than $1.7 million when Heinz's stock soared almost 20 percent after the merger was announced publicly.

(Read more: SEC Looks at Trades a Day Before Heinz Deal)

The emergency court order freezes assets in a trading firm based in Zurich, Switzerland. The SEC said the freeze guarantees that potentially illegal profits can't be taken out of the account while its investigation continues.

According to an SEC official, the suspicious traders will "now have to make an appearance in court to explain their trading if they want their assets unfrozen."

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