The German chancellor joined Instagram in early June and has posted more than 50 pictures to the account.
Many of the pictures have attracted comments in Russian criticising her and praising Russian leader Vladimir Putin.
It is not clear whether the comments are a co-ordinated campaign or just the work of a few activists.
The flood of comments began soon after Mrs Merkel set up the account. The first picture shared via the @bundeskanzlerin account showed the chancellor and her aides preparing for a European Council meeting.
Comments left in Cyrillic or by people with Russian-sounding account names said the image resembled Hitler in his bunker during the closing days of World War Two. Others warned that Russians would "soon be in Berlin again".
Since then, almost every image posted by Mrs Merkel's office of her in meetings and summits has attracted comments in Russian criticising her and her policies. An image of the chancellor talking to Ukrainian President Petro Poroshenko won many abusive comments.
The only positive comments in Russian were added to an image featuring Russian President Vladimir Putin. People leaving comments called him a "great man" and the "best president".
Staff in Mrs Merkel's office have been deleting comments but some remain despite the purge. Many people re-posted their comments once the originals were removed.
The deluge of comments comes soon after Radio Free Europe  and the New York Times revealed that Russia has created at least one "troll factory" that employs people to push pro-Kremlin propaganda and hoaxes via social media in Russia and elsewhere. Some of the 400 or so people employed at the agency also attack people critical of the Russian government.
Russian trolls are targeting Angela Merkel's newly created Instagram account with hostile and critical comments.