The legal action was lodged on Friday after the Chancellor's approval.
The Treasury said the European Union had gone beyond its remit in seeking to regulate bonuses.
An HM Treasury spokesman said: "Britain has been at the forefront of global reforms to make banking more responsible, including big reductions in upfront cash bonuses and linking rewards to long-term success.
"These latest EU rules on bonuses, rushed through without any assessment of their impact, will undermine all of this by pushing bankers' fixed pay up rather than down, which will make banks themselves riskier rather than safer.
"In other words, as the Chancellor has said, they may undermine responsibility in the banking system rather than promote it.
"Regulation of pay in this manner goes beyond what is permitted in the EU Treaty. That's why we are challenging these rules in the European Court, to ensure the legislation respects the EU Treaty and actually achieves what it's meant to. A more stable banking system that serves the economy, businesses and consumers."