Economic weights (EW) for the Slovak dairy production system were calculated in Holstein, Slovak Simmental, and Slovak Pinzgau breeds under a direct support regime using a bio-economic approach. EW were calculated for three scenarios as follows: A: without agricultural subsidies; B: agricultural subsidies included in revenues and C: agricultural subsidies included in feeding costs. Quota-free milk production was assumed in all scenarios. The base price of milk was corrected according to real fat, protein and somatic cell content. Under the given economic and production conditions, only the Holstein system in scenario A was economically profitable. All simulated systems were profit-making when agricultural subsidies were taken into account (B and C). No influence of subsidies on EW of traits in scenario B was found. Most of the evaluated traits (especially milk and functional traits) showed higher marginal economic weights when subsidies were considered in feeding costs (C). Regardless of the scenarios, milk components were of higher relative economic importance for Holstein cattle than for Slovak Simmental and Slovak Pinzgau cattle. The relative EW of mature weight of cows and daily gain of calves mostly declined in scenario C. A meaningful effect of direct subsidy and milk production level on the economic efficiency of Slovak Simmental and Slovak Pinzgau cattle was found. Handling direct subsidy in scenario C seems to be a suitable methodology to avoid the underestimation of EW for milk and functional traits.