Tear gas was used near the Idomeni crossing, where more than 11,000 refugees and other migrants are camped out on the Greek side of the border.
Aid organisation Medecins Sans Frontieres (MSF) said it had treated around 300 injured people.
Balkan states closed off the migrant route to northern Europe this year.
"The indiscriminate use of chemicals, rubber bullets and stun grenades against vulnerable populations... is a dangerous and deplorable act," Greek government spokesman George Kyritsis said.
MSF said authorities had fired tear gas, rubber bullets and stun grenades at those trying to force their way into Macedonia.
"Two hundred people were treated for respiratory problems caused by tear gas, mostly men but including women and some children under the age of five," MSF spokesman Jonas Hagensen told the BBC.
More than 30 people were treated for rubber bullet wounds, he added, and a further 10 people said they had been beaten by Macedonian police.
Some 30 people had been treated for shock and other injuries; seven had been sent to hospital with more serious wounds.
Sunday's unrest reportedly began after a group of migrants approached the fence to ask Macedonian border guards to open it and let them pass.
When their demand was rejected, they were joined by others, some of whom were carrying packed bags.
Migrants could be seen running from clouds of tear gas just inside the Greek border, as well as hurling stones across the fence.
152,461
in 2016, up to 7 April
37% of 2016 arrivals are children
53% arrive on Lesbos
366 died on Turkey-Greece route
853,650 arrivals in 2015
An unnamed Macedonian police official told AFP: "Greek police are using tear gas near the border with Macedonia. It is calm so far on the Macedonian side of the border."
However, Reuters news agency, also quoting an unnamed Macedonian police official, said migrants had thrown stones at the Macedonian police.
"The police fired tear gas in response," the official said.
"The migrants were pushing against the fence but standing on the Greek side of the border. The fence is still there, they have not broken through."
This week Greece began deporting migrants who do not qualify for asylum, under an EU deal with Turkey.
More than 300 people, many of them Pakistanis, were sent to Turkey by ferry from the Greek islands.
In addition, nearly 100 were deported via Greece's land border with Turkey, AFP reports.
The International Organisation for Migration said the rate of arrivals had dropped in the first week of April, with 5 April the first day since last year that no arrivals were recorded.
More than a million undocumented refugees and other migrants have entered the EU by boat from Turkey to Greece since early last year, generating an unprecedented crisis for the EU's 28 member-states.
A note on terminology: The BBC uses the term migrant to refer to all people on the move who have yet to complete the legal process of claiming asylum. This group includes people fleeing war-torn countries such as Syria, who are likely to be granted refugee status, as well as people who are seeking jobs and better lives, who governments are likely to rule are economic migrants.
Greece has condemned the action of Macedonian police to disperse hundreds of migrants at the border between the two countries.