Screens and sound systems at Hanoi and Ho Chi Minh City airports broadcasted anti-Vietnamese and anti-Philippines slogans on Friday taking the Vietnamese officials by surprise.
Vietnam's transport ministry said a Chinese hacker was responsible, BBC reported. Vietnam Airlines' website was also briefly hacked.
Media in Vietnam reported that staff at the airports had to resort to checking in passengers manually, avoiding computers for several hours.
A Chinese woman tourist -- surnamed Zhong from Guangdong province -- has complained that she found an obscenities written on the two pages of her passport depicting China's nine-dash line which signified Beijing's claims over the disputed South China Sea.
An international tribunal has struck down China's claims over the area based on historic rights and upheld the Philippines' claims over the area. China has rejected the verdict.
Besides the Philippines, Vietnam, Malaysia, Brunei and Taiwan have counter claims over the area.
China asked Vietnam to investigate reports that the Chinese visitor's passport was handed back with obscenities written on two pages.
Customs officers at Vietnam's Da Nang airport, not one of those hacked on Friday, have reportedly also confiscated maps featuring the nine-dash line from Chinese passengers, the report said.
A provincial Vietnamese television station stopped airing Shanghai Bund, a Chinese remake of a Hong Kong series, after the show's lead actor voiced his support for Beijing's claims over the South China Sea.
The South China Sea issue is equally sensitive in Vietnam.
China's attempts in the past to conduct oil exploration in the disputed areas of the South China Sea sparked anti-China riots in Vietnam in 2014 in which two Chinese were killed and over a hundred injured.
Over 460 factories, mainly belonging to Chinese investors in Vietnam, were attacked and set fire by mobs.
As the situation became serious, China evacuated over 7,000 Chinese workers back to the country.
China also objected in the past to India's Oil and Natural Gas Commission (ONGC) undertaking exploration at the invitation of Vietnam.
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