The change will see both the Pensions Regulator and the Pension Protection Fund involved in assessing the financial stability of pension schemes.
The Government wants a flat fee levy for the funds due to launch in April but Opposition peers want a risk-based calculation for less sound schemes. Voting was 147-106 in favour of introducing a risk-based levies after the scheme has been operating for a year.
Liberal Democrat Lord Oakeshott joined forces with Tory peer Lord Higgins to lead a vote which beat the Government again on Monday.
Peers voted to ensure that the 400m pledged for the Financial Assistance Scheme to support victims of collapsed pension schemes comes from the Treasury. Voting was 132-110.
Peers also backed a move ruling out any means’ testing of payments by 139-117.
An additional amendment will be tabled next week pushing for the scrapping of compulsory annuity purchase at the age of 75.
Lord Higgins said: “We are all concerned to help those who suddenly find, through no fault of their own, that their prospects for retirement have been devastated.”