In June 1996, Sobchak lost his bid for reelection in Saint Petersburg, and Putin, who had led his election campaign, resigned from his positions in the city administration. He moved to Moscow and was appointed as deputy chief of the Presidential Property Management Department headed by Pavel Borodin. He occupied this position until March 1997. He was responsible for the foreign property of the state and organized the transfer of the former assets of the Soviet Union and the CPSU to the Russian Federation.[39]
On 26 March 1997, President Boris Yeltsin appointed Putin deputy chief of the Presidential Staff, a post which he retained until May 1998, and chief of the Main Control Directorate of the Presidential Property Management Department (until June 1998). His predecessor in this position was Alexei Kudrin and his successor was Nikolai Patrushev, both future prominent politicians and Putin's associates.[39] On 3 April 1997, Putin was promoted to 1st class Active State Councillor of the Russian Federation — the highest federal state civilian service rank.[66]
On 27 June 1997, at the Saint Petersburg Mining Institute, guided by rector Vladimir Litvinenko, Putin defended his Candidate of Science dissertation in economics, titled The Strategic Planning of Regional Resources Under the Formation of Market Relations.[67] This exemplified the custom in Russia whereby a young rising official would write a scholarly work in mid-career.[68] Putin's thesis was plagiarized.[69][70] Fellows at the Brookings Institution found that 15 pages were copied from an American textbook.
On 25 May 1998, Putin was appointed First Deputy Chief of the Presidential Staff for the regions, in succession to Viktoriya Mitina. On 15 July, he was appointed head of the commission for the preparation of agreements on the delimitation of the power of the regions and head of the federal center attached to the president, replacing Sergey Shakhray. After Putin's appointment, the commission completed no such agreements, although during Shakhray's term as the head of the Commission 46 such agreements had been signed.[72] Later, after becoming president, Putin cancelled all 46 agreements.[39]
On 25 July 1998, Yeltsin appointed Putin director of the Federal Security Service (FSB), the primary intelligence and security organization of the Russian Federation and the successor to the KGB.[73]