Indonesia's government has struggled to hire and train staff quickly enough to oversee its fast-growing aviation market, which the International Air Transport Association expects to triple in size by 2034.
"Until they resolve this they cannot do the same level of supervision and certifications as a country with a robust system in place," one of the sources said.
Since the 2014 audit, Indonesia has come up with a plan to address its problems, the source said.
"They have been very active in developing their plan," the source said. "They are making progress."
But ICAO's auditors would not return to check on the country's progress or run a fresh assessment until the majority of problems found in a previous audit have been fixed.
Indonesian officials based in Canada could not be reached for comment. ICAO did not immediately comment.
The Montreal-based ICAO publishes audit scores online, but typically does not disclose the specific problems behind the scores.
In the audit carried out in May 2014, Indonesia scored below the global average in each of eight categories. The vast majority of countries score above average on at least some categories.
Its lowest score was for "organization", at 20 percent, where the global average is 64 percent. "Accident investigation" was 31 percent, compared with an average of 55 percent. Its best score was for "airworthiness", at 61 percent, compared with an average of 74 percent.
But the audit did not flag any specific "significant safety concerns", the most serious problems. Thailand's most recent audit, for example, uncovered significant safety concerns, prompting several nearby countries to stop its airlines from adding new routes.
In January, an AirAsia (AIRA.KL) flight went down in the Java Sea off Indonesia, killing all 162 aboard. In June, more than 100 people died in the crash of a military transport plane, prompting Indonesia's president to promise a review of the ageing air force fleet.