Federal Parliament has passed a package of changes to its own rules and procedures, but only after the government lost its first vote.

Pregnant Labor minister Tanya Plibersek was absent from the chamber but Opposition Leader Tony Abbott's office said she had been paired with a Coalition MP and that pairing was not an issue.

Ironically, a division over how to deal with divisions in which an MP inadvertently misses a vote was won by the opposition by a single vote.

However, the rest of a package of changes, which the government proclaimed "a great day for parliamentary reform", was passed without controversy.