Alarm Phone on Sunday night accused the Maltese authorities of refusing to order rescue operations for two boats in distress in its search and rescue zones.
It said on Twitter that Malta's non-assistance risked 60 lives on two boats in distress.
A nearby merchant vessel plus #LifeSupport of @emergency_ong had offered support but Malta refused to order a rescue operation, the organisation said.
It pointed out that the weather was deteriorating quickly and rescue was needed immediately.
Earlier this week, a top Italian politician an Italian politician expressed frustration at Malta's unwillingness to rescue migrants, saying the country is "pretending not to see" people at sea.
Malta has rescued just one migrant this year while the number rescued by Italy has tripled to over 30,000, data collected by the UNHCR indicates.
Maltese authorities deny the existence of any plan to systematically ignore rescue calls.