UBS and Credit Suisse are both based in the country, which recently voted in a referendum to give shareholders binding votes on executive pay after a series of rows over large compensation packages.
Credit Suisse paid an average of €214,541 (£184,380) to its staff in 2012, while UBS followed closely at €191,646.
Both those lenders had total wage, salary and bonus bills of more than half their revenues.
German giant Deutsche Bank was next with an average payout of €134,782 and a compensation ratio of 40.55 per cent.
It is the first EU-based bank in the list and so the first to be in line to be hit by the EU’s incoming bank bonus rules which limit variable pay to the same level as fixed pay.
Bank of America came fourth with an average of €98,578, followed by British institution Barclays at €91,935. Both the lenders had compensation ratios well below the 50 per cent mark.
Lloyds, RBS and HSBC all came well down the list after squeezing bonuses in the years since the financial crisis.