The two countries had already agreed in January to strengthen military ties when Niger Prime Minister Ali Lamine Zeine led a delegation to Moscow.
Niger, one of the world's poorest countries, had been a frontline partner of the West in battling jihadists in the Sahel but has embraced Russia as a fledgling defence partner since the elected president was ousted last year.
The two heads of state "talked of the need for strengthening security cooperation... to face current threats," said the Nigerien communique read out on public radio.
They also discussed "projects for multi-sector and global strategic cooperation," it added without further explanation.
A statement from the Kremlin added the two expressed "readiness to start a political dialogue and to develop mutually beneficial cooperation in various fields."
"There was also an exchange of views on the situation in the Sahara and Sahel regions, with an emphasis on coordinating actions to ensure security and combat terrorism," Moscow said.
General Tiani, who has led Niger since the July coup, thanked Putin for Russia's "support" for the Sahel country and its struggle for national sovereignty.
A Russian delegation also visited Niger last December.
The United States still stations some 1,000 troops in Niger although movements have been limited since the coup and Washington has curbed assistance to the government.
A senior US delegation went to Niamey in mid-March to renew contact with the junta, but said they failed to meet Tiani.
The new regime has denounced military cooperation with the West, shunning colonial ties with France.
Niger had previously been an important base for France's military efforts to quell Islamist extremism stemming from the Sahel region.
Niger joined neighbors Mali and Burkina Faso at the start of the month in announcing the creation of a joint force to battle the long-running jihadist rebellions raging in the three nations.
They had announced in January their intention to withdraw from regional bloc the Economic Community of West African States (ECOWAS).