Vietnam has accused the Indonesian navy of firing shots at its fishing vessels over the weekend injuring four of its fishermen in the South China Sea.

However, Jakarta has denied the allegations and said its warship KRI Wiratno-379 fired warning shots when two Vietnamese boats were intercepted four nautical miles inside Indonesian waters. It is thought to be the second clash between the two sides in the hotly contested waters in two months.

The shots were only fired toward the bow of the vessels, The Associated Press cited Indonesia Navy spokesman Gig Jonias Mozes Sipasulta as saying.

Vietnam gave a different account of the incident and said its fishing vessels were very much within the country's sovereignty.

The country's Binh Din newspaper quoted boat captain Nguyen Thanh Ngoc as saying that the vessel was sailing about 100 nautical miles southeast of Con Dao island when it came under attack and that four of the fishermen suffered injuries. Two of them are reportedly shot and wounded seriously.

Indonesia is reported to be notorious for blowing up foreign boats that are caught fishing illegally in its waters. And, the world's largest archipelago nation has taken a tough stance against illegal fishing since President Jokowi Widodo took office in 2014.

Around 200 fishing boats – from China, Vietnam, Malaysia, Nigeria – are all reported to have been blown up since, while the fate of over 20 others awaits court rulings.

In several occasions, it has been the Vietnamese vessels that have come under attack in the South China Sea, where Beijing has claimed almost all of the territories engaging in a dispute with several Southeast Asian countries – Brunei, Vietnam, Malaysia, Taiwan and the Philippines.

Although Indonesia is not directly involved in the territorial dispute in the heavily contested waters, it is reported to be anxious about the presence of even Chinese fishing boats near the Natuna islands, which Jakarta claims as part of its exclusive economic zone. Beijing has reportedly attempted to include this island in its territorial maps in the past.

The Southeast Asian country, which has more than 13,000 islands, renamed the southernmost reaches of the South China Sea as the North Natuna Sea.