[6][7] In his first press statement as Minister of Foreign Affairs, Lipavský stated that his political priorities would be improvement of the Czech Republic's international reputation in the area of human rights, alliance obligations, and international partnerships:[8] The government's program statement calls for a return to a value-oriented foreign policy and the restoration of the good name of the Czech Republic as a country that stands on the side of human rights.

Concrete steps in its implementation will therefore include, for example, the submission of the so-called Magnitsky Act, which will ensure better enforcement of protection human rights.

At the same time, it is necessary to prepare the presidency of the Council of the EU, which the Czech Republic will take over in the middle of next year.Lipavský chose the former ambassador to Kuwait, Martin Dvořák, as his political deputy at the Ministry of Foreign Affairs.

[12][13] In September 2022, Lipavský spoke at the United Nations General Assembly, where he condemned Russia over the annexation of Crimea, the invasion of Ukraine, and human rights violations.

[14] Lipavský supported EU sanctions against Iranian officials and entities in response to Iran's violent crackdown on the Mahsa Amini protests.

[15] At the end of October 2022, Lipavský travelled to Qatar for a two-day visit to lead negotiations over the supply of natural gas,[16] and with the aim of improving the environment for business investments.

He met with the President Isaac Herzog and Israeli Minister of Foreign Affairs Eli Cohen to express the Czech Republic's full support for Israel and offer aid.

[23] On 11 March 2024, ANO leader Andrej Babiš sent an email requesting compromising information on Jan Lipavský and his family, including his children.

[27] On 15 November 2024, students at University College London (UCL) protested the visit of Jan Lipavský, criticizing the Czech government's support for Israel.

"[34] In February 2023, Lipavský declared at a UN Security Council meeting: "Together, we must defend the UN Charter and ensure that war crimes are held accountable under international law.

[40] During the visit of the Turkish foreign minister Mevlüt Çavuşoğlu to Prague in June 2022, Lipavský stated there is a need for a "thorough dialogue" on issues where it is not easy to find an agreement between Turkey and the EU, such as migration or respect for the rule of law.