Lebanon has been without a president since May 2014, when Michel Sleiman's mandate expired, because the country's Christians, Sunni and Shiite Muslims and Druze cannot agree on a candidate.
The country has also not held a parliamentary election since 2009, with the legislature instead twice extending its own mandate.
"This government has become uncontrollable and detrimental" to the interests of the country, Phalange party leader Sami Gemayel said.
"Its existence is worse than its inexistence. Nothing justifies our participation," he told a news conference.
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Those stepping down are Sejaan Azzi (labour) and Alain Hakim (economy and trade).
"The government does not care about finding a solution to the problem of Syrian refugees, nor does it care about the economic plan presented by the economy minister" or the garbage crisis, Gemayel said.
Lebanon currently hosts more than a million Syrian refugees -- nearly a quarter of its own population of four million before the conflict in neighbouring Syria began in 2011.
The country is also going through a "garbage crisis" caused by the closure of its main landfill.
Because Lebanon does not currently have a head of state, the two ministers are unable to present their resignations formally, and have instead chosen not longer to exercise their functions.