Underlying net profit after tax was A$30 million, down from $564.5 million for the 2019 financial year.
However, the result was in line with analyst forecasts.
Underlying EBITDA was down 71% to $306 million, while operating cashflow dropped 84% to $146.4 million.
The result was attributed to weaker coal prices, the impacts of labour shortages, dust events at Maules Creek, and the eight-week Narrabri longwall move.
Whitehaven CEO Paul Flynn said the significant contraction in coal prices disproportionately impacted its headline financial results.
"Our immediate focus is on achieving greater efficiency and more consistent operational performance in anticipation of markets rebalancing and price improvements beginning to flow through," he said.
"We are confident about the continuing demand for high quality coal in a more carbon conscious world and the major role it will play as part of the global economic recovery."
Disruption due to drought and bushfires and the impact of unmapped historical underground workings at Whitehaven's Werris Creek also contributed to a 4% drop in FY2020 run-of-mine coal production to 16.6 million tonnes.
Flynn said the NSW government's recent approval of the company's Vickery extension project was a significant achievement, however, the company was bracing for further headwinds brought about by the global COVID-19 pandemic.
The Vickery project is a proposed open cut mine with a 20-year mine life in the Gunnedah Basin with marketable reserves of 178Mt.
The mine will produce a majority metallurgical coal for steel-making, with the balance being high quality thermal coal destined for premium export markets in the Asian region.
"Given continuing short-term economic uncertainty, we remain cautious about expansion and capital allocation," Flynn said.
Net debt rose from $161.1 million to $785.7 million over the year, while gearing jumped from 4% to 20%.
The company had $468.8 million of available liquidity at June 30.
Guidance for FY21 is 18.5-20 million tonnes of managed coal sales.
Unit costs, excluding royalties, are forecast at $69-74/t.
Bell Potter Securities analyst Stuart Howe had expected guidance to be stronger.
He retained a buy rating but lowered his target price by 5c to $2.25.
"Whitehaven's improved operational outlook for FY21, thermal coal markets appearing to have stabilised and Whitehaven's growth opportunities should markets recover, all support our buy recommendation," he said.
Whitehaven shares finished the week at 90c, a four-year low. The company is valued at about A$920 million.