Tropical Cyclone Veronica disrupted Pilbara mining and shipping for several days last month and caused some damage to the Cape Lambert A port facility.
It followed a fire at the same facility in January.
Rio was forced to declare force majeure on certain contracts and warned that around 14 million tonnes of production would be lost this year.
The company had warned earlier this month that 2019 shipments were likely to be at the lower end of the 338-350Mt guidance.
Today, it lowered full-year guidance to 333-343Mt after recovery work was hindered by Tropical Cyclone Wallace.
Shipments for the March quarter were down 14% year-on-year and 21% quarter-on-quarter to 69.1Mt.
The company warned a recovery in the current quarter would remain subject to weather.
Rio already suffered a setback this month with a minor fire in a screen house at the East Intercourse Island port, though operations have restarted.
The company left its 2019 cost guidance of US$13-14 per tonne unchanged.
"Our iron ore business faced several challenges at the start of this year, particularly from tropical cyclones," Rio CEO J-S Jacques said.
"The quarterly operational performance in our other products was solid, generally higher than last year.
"Our focus remains on safety, delivering our ‘value over volume' strategy and allocating capital with discipline, to continue delivering superior returns to our shareholders in the short, medium and long-term."
In copper, March quarter mined production was 144,000 tonnes, 3% higher year-on-year, due to strong contributions from Oyu Tolgoi in Mongolia and Kennecott Utah.
Rio provided further details on delays at the Oyu Tolgoi underground project.
Commissioning of the main production shaft (Shaft 2), previously expected by the end of March, is now due for completion in October.
Bauxite and titanium dioxide slag production was slightly higher than the same time last year, while aluminium production was flat.
Despite the flat-to-negative quarterly results, Rio's shares broke through A$102 for the first time since early July 2008, peaking at $102.83.
RBC Capital Markets analyst Paul Hissey noted the strength of the iron ore price, with the MySteel 62% Australian fines index currently at US$95.80 per tonne.
"Whilst softer Pilbara iron ore shipments in isolation should derive earnings downgrades, the iron ore division continues to generate significant cashflow with prices at current levels," he said.
"We continue to flag downside risks to iron prices through 2019 and this predicates our underperform rating on Rio."
RBC has a A$66 price target for Rio.
Rio shares last traded 1.6% higher at $102.34.
