Safety assessments for risky air routes are "not good enough", according to the British Airline Pilots Association.
Balpa general secretary Jim McAuslan said there must be "a uniform level of safety, not one decided in secret".
His comments come after a Malaysia Airlines plane crashed over Ukraine.
Balpa has also called for "global leadership" from the International Civil Aviation Organisation (ICAO) in flight operations that are in or over areas of hostility.
Although airlines are no longer flying over Ukraine - where separatists are controlling parts of the east - passenger planes have flown over areas of northern Iraq and Syria in the past week, where there is ongoing conflict.
Some US and European airlines, including the UK's Easyjet, have suspended flights to Israel after a rocket landed one mile (1.6km) away from Tel Aviv airport.
Mr McAuslan said: "Individual pilots looking at their flight plans need to have absolute confidence that the right calls are being made.
"The process behind the choice of airspace routing is based on a risk assessment, both by a country's national aviation security services in the advice that they give to their airlines, and by the airline in how they assess this advice.
"This risk assessment approach can give an illusion of safety but it is in fact vulnerable to all sorts of influences including commercial pressure and so it is not surprising to us that there are differences in the way that this risk is assessed by different airlines."
Mr McAuslan also said while the "ultimate responsibility of last week's murders" lies with those who apparently directed a missile at flight MH17, this should not prevent the failures which "led to that outcome, failures that could easily be repeated in other areas of conflict".
A total of 283 passengers, including 80 children, and 15 crew members were on board flight MH17. There were no survivors from the crash and the exact cause has not yet been determined.
Balpa also says although ICAO is the United Nations body responsible for co-ordinating the safety and order of global aviation, it should have a greater leadership role and strengthened powers to go with that responsibility.
Mr McAuslan added: "ICAO's purpose should be to lead where national authorities cannot and it should have the tools to do that.
"The problem of the absence of a clear international co-ordination to avoid operations above eastern Ukraine has now become tragically obvious and to avoid a repeat ICAO should be better resourced and enabled to declare airspace unsafe."
ICAO also needs to reflect on its own rules of membership, Mr McAuslan added.
"Participating states enjoy privileges such as free movement, but with that comes responsibility.
"If a state does not live up to that responsibility, such as sharing of information and allowing full and free access to accident investigation, then membership and privileges should be reconsidered."