Edinburgh-based Cairn's annual report shows Mr Thomson received remuneration of £962,765 in 2013 compared with £1,018,570
The cut in remuneration was largely the result of a big drop in the bonus he was paid in 2013, to £330,750 from £426,487 in the preceding year.
Cairn said executive directors had received half the maximum bonus payable under the main criterion, covering efforts to make new finds and appraise discoveries. The report says exploration and appraisal drilling were "relatively disappointing versus targets".
Renowned for making bumper finds in India in the first decade of the century, Cairn has yet to repeat that success on the acreage it has amassed since in areas like Greenland and Morocco.
Mr Thomson's salary increased by 6.5% annually, to £525,500 in 2013, from £494,000 in 2012.
The total remuneration of deputy chief executive Dr Mike Watts fell by 9%, £83,658, to £836,543 in 2013 from £920,201.
Jan Brown, managing and finance director, earned £784,474, down 9%, £74,640 on the £859,114 earned in the previous year.
Mr Thomson was awarded shares worth £1.6m under the company's Long Term Incentive Plan in 2013, subject to a three year performance period.
None of the LTIP shares awarded to directors in
2010 vested in 2013 as the performance conditions were not met.
Mr Watts and Ms Brown were awarded shares worth £1.4m and £1.3m respectively under the LTIP in 2013.
Mr Watts and Ms Brown will stand down as executive directors at next month's general meeting. They will work out notice periods of 12 and six months respectively while Cairn tries to resolve a tax dispute in India.
Sir Bill Gammell, the founder of Cairn Energy who will stand down as chairman following the AGM, earned fees totalling £236,000 in 2013, versus £226,971 in 2012.
Cairn suffered a 67% vote against its directors' remuneration report for 2011, in spite of scrapping a proposed one-off share option award worth £2.5m for Sir Bill that had drawn criticism. The 2012 report won the support of 99.51% of votes cast.