HIE, which owns the funicular, had also been pursuing a payment from a former operator of the facility.
The UK's highest railway reopened in January after four years out of action.
It had been shut down because of structural problems.
HIE had been pursuing legal action in the Court of Session against construction company Galliford Try Infrastructure Ltd and designer AF Cruden Associates Ltd over work done in the 1990s and early 2000s.
It had also sought payment relating to guarantees issued by Natural Assets Investments Ltd, the parent company of CairnGorm Mountain Ltd (CML), which had operated the funicular on HIE's behalf.
HIE chief executive Stuart Black said the agency was pleased to have reached a settlement.
The railway was built at a cost of £19.5m and was opened in 2001. It connects a base station with a restaurant and a ski area 1,097m (3,599ft) up Cairngorm mountain.