Caritas and World Vision are among the signatories of the document, published before European Union heads of states begin a two-day European Council summit on Thursday.
It said: "Your decisions have life and death consequences, and if you continue to lower standards, countries around the globe will follow suit."
Meeting in Brussels, leaders will review progress since the adoption of the Malta Declaration last month, an agreement which sought to stem the flow of migrants from Libya to Italy, particularly through greater co-operation with Libyan authorities.
160 organisations remind EU leaders they must protect people on the move https://t.co/I4msv3XJMF pic.twitter.com/ohLVrp5Qtn
— World Vision EU (@WorldVisionEU) March 8, 2017
More than 181,000 thousand people illegally entered Europe via the so-called Central Mediterranean route last year, while the number of people dead or missing after trying to make the journey has reached a new record each year since 2013.
The letter claimed too many leaders have been "pre-occupied" with stopping people from reaching Europe, at the risk of shutting out people who need assistance most.
The statement continues: "We expect statesmanship that stands up for humanity and dignity and that addresses people's fears, instead of fuelling them."
Many of those trying to make the perilous journey to Europe via the Mediterranean Sea have come from war-torn countries such as Syria and Iraq, or nations like Eritrea where the UN human rights abuses are being committed.
The letter goes on to say: "We expect sustainable, long-term migration policies that guarantee respect for people's rights rather than pushing them into danger."
"Further, if the EU and its member states want to remain credible international actors, they cannot expect countries like Turkey, Jordan and Lebanon to host millions of refugees, while simultaneously pushing migrants and refugees back at EU borders, stranding thousands in inhumane living conditions on the Greek islands, or pushing them back into an uncontrolled conflict zone like Libya."