Comments by Iran's Foreign Minister Hossein Amir-Abdollahian come as tensions are rising between his country and Azerbaijan, which heavily relies on Israeli weapons.
Iran said that it has "serious concerns" about Israel's presence in the Caucasus, as tensions mount between Iran and Azerbaijan over Baku's ties with Israel, a major arms supplier.
The comments came a day after unconfirmed reports in Azerbaijani media said Iran has closed its airspace for Azerbaijani army aircraft.
"We certainly will not tolerate geopolitical change and map change in the Caucasus," Iranian Foreign Minister Hossein Amir-Abdollahian told reporters in Moscow.
"We have serious concerns about the presence of terrorists and Zionists in this region."
Since mid-September, tensions have soared between Iran and Azerbaijan, which share a 700-kilometre (430-mile) border.
Israel is a major arms supplier to Azerbaijan, which last year won a six-week war with neighbour Armenia over the disputed Nagorno-Karabakh region.
#Iran FM @Amirabdolahian: We have concerns about the South Caucasus. I shared these concerns with [#Russia FM] Mr Lavrov. We do not accept any geopolitical change in the Caucasus, and we are seriously concerned about the presence of terrorists and Zionists in the region.— Abas Aslani (@AbasAslani) October 6, 2021
On Friday, Iranian ground forces began manoeuvres near the frontier, a move criticised by Azerbaijani President Ilham Aliyev.
The day before the drills were launched, Amir-Abdollahian told his Azerbaijani counterpart that Iran would not tolerate Israel's presence or activity "next to our borders" and vowed to take any necessary action.
Aliyev said Tuesday that Baku "will not leave unanswered" Tehran's "baseless" accusations of an Israeli military presence on its soil.
Also Wednesday, Azerbaijan's state-owned AZAL airlines said that it will start using Armenian airspace for flights.
The move marked the first sign of easing tensions between Baku and Yerevan, days after the countries' leaders expressed readiness to meet for talks.
Iran closes its airspace for Azerbaijani flights, while Armenia opens its airspace to Azerbaijan.— Shujaat Ahmadzada (@shujaaatA) October 6, 2021
'Nuclear talks in Vienna to restart soon'
Meanwhile, Abdollahian said in Moscow on Wednesday that he expects negotiations on the Iran nuclear deal to restart in Austria soon.
"We are now finalising consultations on this matter and will soon restore our negotiations in Vienna," he told reporters after talks with Russian Foreign Minister Sergei Lavrov.
The 2015 nuclear deal gave Iran sanctions relief in return for tight controls on its nuclear programme.
In 2018, then-US President Donald Trump withdrew from the multilateral accord and began reimposing sanctions.
Tehran has gradually rolled back its nuclear commitments since 2019.
US President Joe Biden reversed Trump's decision to pull the United States from international negotiations on curbing Iran's nuclear ambitions.
But talks in Vienna to revive the deal have been at an impasse since June, when Iran's ultraconservative new President Ebrahim Raisi was elected.