By Hyonhee Shin

SEOUL (Reuters) -South Korean President Yoon Suk Yeol on Monday blamed authorities' failure to follow disaster response rules as the death toll from days of torrential rain rose to 40, including a dozen people found dead in a submerged underpass.

Deluges have pummelled central and southern regions since Thursday as the rainy season that started in late June reaches its peak. The interior ministry has also reported nine people missing and 34 injured across the nation.

Twelve deaths, including three bodies found overnight, occurred in a tunnel in Cheongju, 110km (68 miles) south of Seoul, where 16 vehicles, including a bus, were swamped by a flash flood on Saturday after a river levee collapsed.

The incident fuelled questions over South Korea's efforts to prevent and respond to flood damage. Some drivers who use the road regularly blamed the government for failing to ban access to the underpass even though floods were widely forecast.

Yoon, just back from an overseas trip, on Monday convened a disaster response meeting and conceded the situation was made worse because of poor management of vulnerable areas.

"We've repeatedly emphasised access control over dangerous areas and preemptive evacuation since last year, but if basic principles of disaster response are not kept on the spot, it is difficult to ensure public safety," Yoon told the meeting.

Nearly 900 fire, police and military officials took part in the underpass rescue operation, using boats, underwater drones and other equipment, according to the interior ministry.

Seo Jeong-il, fire chief in west Cheongju, told a briefing on Monday that while search efforts continued there were no signs of more victims in the remaining vehicles in the tunnel.

Floods have claimed dozens of lives during recent rainy seasons as weather patterns have become more extreme.

The government last year vowed to take steps to better cope with climate change-induced disasters after the heaviest downpours in 115 years pounded Seoul, including the glitzy district of Gangnam, leaving at least 14 dead and flooding subways, roads and homes.

Yoon on Monday flew in a helicopter over some devastated areas. Earlier, he called for utmost efforts to rescue any remaining victims and vowed support for those affected, including designating flood-hit areas as special disaster zones.

"The government will restore everything, so don't worry too much," Yoon said after meeting residents in Yecheon in North Gyeongsang province, an area hit by landslides where 19 people died and eight remain missing.

The situation across the border in North Korea remains unclear, but in recent weeks state media has reported on heavy rainfall and referred to measures to protect crops in a country that has suffered from serious food shortages.

At a briefing, the South's Unification Ministry said it had asked Pyongyang to notify Seoul of any plans to release water from its Hwanggang Dam. In 2009, the release of water from the dam resulted in flooding downstream that killed six South Koreans.

(Reporting by Hyonhee Shin; Additional reporting by Hyunsu Yim; Editing by Ed Davies, Tom Hogue and Lincoln Feast)