The four countries cut off diplomatic and transport links with Qatar on June 5, accusing the Qatari government of supporting extremist groups, interfering in their internal affairs and seeking closer ties with Iran.
Qatar has filed a complaint with the World Trade Organization over an "illegal siege" imposed by its Persian Gulf Arab neighbors, the commerce ministry said.
Qatar has repeatedly denied their accusations.
The WTO suit does not include Egypt, the fourth country involved in the boycott.
Qatar has been put under pressure by the embargo, and the gas-rich nation has been forced to engineer alternative supply chains.
The complaint could mark the first formal step in the WTO's dispute resolution process, which would force the countries to sit down and negotiate with Qatar. If an agreement is not reached within 60 days, the WTO will convene a dispute settlement panel.
The text of Qatar's WTO complaint cites "coercive attempts at economic isolation" and spells out how the blockading countries are impeding Qatar's trade rights.
In its WTO case, Qatar would also draw attention to the impact the boycott was having on other WTO members, he said.
The boycotting states cut ties with Qatar - a major global gas supplier and host to the biggest USA military base in the Middle East - on June 5, accusing it of financing militant groups in Syria, and allying with Iran, their regional foe, allegations Doha denies.
The countries have sought to extract concessions from Qatar in return for restoration of diplomatic and economic ties.
In comments to Qatar-based Al Jazeera, Qatar's Transport and Information Minister said the boycotting countries had discriminated against Doha in violation of an global agreement guaranteeing overflights.
Last month, foreign ministers of the quartet said they are ready to begin talks, if Qatar shows willingness to halt support for terrorism and abide by their demands.
"Dialogue doesn't mean there are concessions", said Saudi Foreign Minister Adel Al-Jubeir.