Pashinyan had come under pressure with thousands of demonstrators protesting since Tuesday and demanding he resign over a ceasefire that secured territorial advances for Azerbaijan in Nagorno-Karabakh after six weeks of fighting.
The NSS said its former head Artur Vanetsyan, the former head of the Republican Party parliamentary faction Vahram Baghdasaryan and war volunteer Ashot Minasyan were under arrest.
"The suspects were planning to illegally usurp power by murdering the prime minister and there were already potential candidates being discussed to replace him," the NSS said in a statement.
Pashinyan said earlier this week he had no choice but to sign the agreement to prevent further territorial losses. He said he was taking personal responsibility for the setbacks, but rejected calls to step down.
The ceasefire halted military action in and around Nagorno-Karabakh, an enclave internationally recognised as part of Azerbaijan but populated by ethnic Armenians. Under the agreement, 2,000 Russian peacekeeping troops are being deployed to the region.
Since the early 1990s, ethnic Armenians had held military control over all of Nagorno-Karabakh and substantial swathes of Azeri territory surrounding it. They have now lost much of the enclave itself as well as the surrounding territory.
