The 39% drop was unexplained on Tuesday, but it could reflect sanctions imposed in May 2004 by the United States, which accuses the country of supporting terrorism and undermining efforts to stabilise Iraq.
The sanctions restrict the dealings US-based banks can have with their Syrian counterparts.
Major Swiss banks, which have extensive operations in the US, may have heeded the sanctions.
Spokesmen for the largest banks, UBS and Credit Suisse, declined to comment.
The Syrian assets in 106 Swiss banks dropped by the end of last year to 8.6 billion francs from 14.1 billion francs at the end of 2003, according to the statistics of the Swiss National Bank.
The national bank report gave no reason for the decline.
The lion's share of Syrian assets in Switzerland previously were deposited in the two or three largest Swiss banks.
At the end of 2003 they had Syrian assets worth 13.5 billion francs.
No figure for the big banks is given for the end of 2004, but national bank spokesman Werner Abegg said there had been statistical problems and that it should not be assumed that the assets had dropped to zero.
But the US Treasury Department put the state-owned Commercial Bank of Syria, the largest financial institution in the country, on its black list as an alleged money-laundering centre for so-called terrorists and the former government of Saddam Hussein.