Piotr Mueller told private broadcaster Radio Zet on Monday that the government will "direct financial resources" to these areas.
Last Thursday, President Andrzej Duda declared a 30-day state of emergency in regions bordering Belarus, in a move designed to stem the flow of migrants crossing into Poland.
Under the state of emergency, non-residents are prohibited from entering the areas it covers, dealing a blow to sectors such as tourism.
Mueller said the amount of compensation paid would be based on what entrepreneurs earned in the corresponding period in previous years.
"At the moment, we are working out a mechanism. We will subject it to quick consultations so that these people do not lose out," Mueller said.
Earlier on Monday, Deputy Interior Minister Maciej Wasik said that later this week the government will present measures for compensating companies that have lost income because they cannot host tourists in the areas covered by the state of emergency.
"I am convinced these will be measures that are satisfactory for the tourism industry," he added.
Poland has accused the government of Alexander Lukashenko, the Belarusian president, of pushing migrants from the Middle East across the its border in retaliation for sanctions that Brussels has imposed on Minsk. (PAP)