Secretary of State for Sport Miguel Cardenal, who was appointed after the centre-right People's Party won a general election late last year, said the plan would be presented on Wednesday.
"It is not possible to say all the professional teams have outstanding debts with the tax authorities," Cardenal said at a Europa Press event in Madrid.
"Those that do, for the most part, have their debts sorted out into payment plans with conditions, just like any other Spanish business might do," he added.
"Over the last few weeks the (government) and the LFP have had meetings and they have reached their conclusion.
"We hope (the plan) will put a break on the growth of this debt and that it will disappear in a few years. Probably by 2020 this problem will have been effectively resolved."
The government is keen to wipe out the clubs' tax debts as part of a sweeping austerity drive aimed at meeting fiscal targets agreed with the European Union.
Cardenal said last month clubs also owe around 600 million to the social security system.
"This wasn't a negotiation, because there was absolutely no resistance on the part of the LFP and they want to correct the situation as well," Cardenal said.
"The league aren't happy with this situation because it affects the fairness of the competition and their reputation and image," he added.
Many clubs have slipped deeper into the red in recent years as they struggle to pay spiralling wage and transfer costs and some have been forced into administration following a futile struggle to remain competitive.
A study published this month by a professor of accounting at the University of Barcelona showed the 20 clubs in Spain's top division had combined debts of some 3.53 billion euros at the end of last season, up from 3.43 billion a year earlier.
With around 550 million owed by the 22 teams in the second tier, Spanish professional soccer is more than four billion euros in the red.
Real Madrid and Barcelona, the world's richest clubs by income, both have debts of close to 600 million euros, according to Gay's research, while Atletico Madrid owes more than 500 million and Valencia almost 400 million.