After flying over the Main river in Frankfurt, the two activists landed at the low-rise ECB complex and unfurled a banner that demanded the ECB "stop funding climate killers".
An ECB spokesperson confirmed the breach and said that police had been called. He added that the bank was conducting a review of its strategy and this process included an in-depth analysis of how to respond to the climate crisis.
A Greenpeace spokesman acknowledged that ECB President Christine Lagarde was in favour of changing the bank's policies but said she faced opposition.
"We demand an about-turn and it should be made clear that the biggest hindrance to more climate-friendly policies here in Germany is coming from the German Central Bank in the form of Jens Weidmann who is still blocking a climate-friendly fiscal policy," Greenpeace spokesman Mauricio Vargas said.
The Greenpeace protest followed a think tank report which argued that the ECB's lending rules, particularly it's collateral requirements, favoured carbon-intensive industries and perpetuated a market failure to properly price polluting assets.
Vargas named companies such as Shell, Total, Lufthansa who benefit from ECB programmes.