The Iran-backed Huthis have been targeting merchant vessels transiting the vital Red Sea trade route for months but Wednesday's deaths were the first reported fatalities resulting from such an attack.
"The Department of Foreign Affairs expresses its sincere condolences to the families of the two Filipino crew members of the civilian bulk carrier True Confidence, which was the subject of a missile attack from Houthi rebels in Yemen," the ministry said in a statement.
The Indian Navy rescued 21 of the ship's crew, including 13 Filipinos, and brought them to Djibouti, "where three of them are in the hospital due to serious injuries", the statement added.
The Philippines' Department of Migrant Workers earlier reported four Filipino casualties of the missile attack -- two dead and two injured.
The missile struck the ship's fuel tanks, causing a fire and killing the two Filipinos and injuring two other compatriots among others, Department of Migrant Workers Undersecretary Hans Cacdac said in an interview with local media.
A fifth Filipino suffered minor injuries during the ship's evacuation, which "was rushed because the ship was on fire", he told ABS-CBN television network.
The US military said the crew reported three dead and four wounded, three of them critically, from the anti-ship ballistic missile that struck the Barbados-flagged, Liberian-owned M/V True Confidence, which suffered significant damage.
Huthi military spokesman Yahya Saree wrote on social media that the True Confidence was targeted with missiles "after the ship's crew rejected warning messages" from the rebels.
The Huthis began attacking ships in the Gulf of Aden and the Red Sea last November, a campaign they say is intended to signal solidarity with Palestinians in Gaza.
Manila is still seeking the release of 17 Filipinos taken hostage by the Huthis in November after the rebels seized their ship in the Red Sea.
cgm/dhw
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