TOKYO -- Two decades after issuing a joint declaration pushing for the creation of a "future-oriented" relationship, Japan and South Korea are still struggling to put their history behind them as long-running disputes over wartime "comfort women" and other topics flare up again.

"Japan and South Korea are neighbors, and we have many difficult issues because of that," Japanese Prime Minister Shinzo Abe said Tuesday at an event in Tokyo to commemorate the countries' 1998 Joint Declaration. "Political leaders need to make big decisions in order to overcome these issues."

The declaration was a key turning point in bilateral relations, with then-Prime Minister Keizo Obuchi offering "deep remorse and heartfelt apology" for the "tremendous damage and suffering" caused to the South Korean people through Japan's colonial rule. For his part, then-South Korean President Kim Dae-jung said "the present calls upon both countries to overcome their unfortunate history and to build a future-oriented relationship."

Bilateral ties cooled temporarily in 2012, when then-South Korean President Lee Myung-bak set foot on a group of disputed islands called Takeshima by Japan and Dokdo by South Korea. But the countries appeared to turn over a new leaf with a 2015 deal intended to put the comfort women issue "finally and irreversibly" to rest.

And yet, another three years later, Japan and South Korea are once again at loggerheads. In a summit with Abe last month, President Moon Jae-in said many South Koreans want to disband the Reconciliation and Healing Foundation -- a body created to help former comfort women as part of the 2015 deal.

Japan originally contributed 1 billion yen ($8.85 million at current rates) to the foundation under the terms of their agreement, but the South Korean government in July decided to replace that money with its own funds.

South Korean protesters rally around a statue honoring wartime "comfort women" against a bilateral deal signed with Japan to put an end to the issue in December 2015. The agreement has been highly unpopular among the South Korea public. © Reuters

Tokyo strongly opposes any departure from the 2015 agreement. "It is important that we steadily carry out the Japan-South Korea deal," a Japanese government source said. "We will persistently express our position to the South Korean government."

Another sticking point is the lawsuits by South Koreans forced to work for Japanese companies during the colonial era, which have largely stalled since the Seoul High Court in 2013 ordered Nippon Steel & Sumitomo Metal to pay 400 million won ($352,000 at current rates) to its former laborers. The South Korean Supreme Court has recently begun deliberating whether to hear appeals on Nippon Steel and on a separate case involving Mitsubishi Heavy Industries.

These companies could have their assets seized to pay the workers. Given that Japan believes its 1965 peace treaty with South Korea resolves the issue of wartime reparations to individuals, bilateral ties may be dealt a heavy blow.

The use of the rising sun flag by Japan's Maritime Self-Defense Force vessels has also become a hot topic recently. The flag, also used by the Japanese military during World War II, is considered a symbol of the country's aggression in South Korea and China. Japan decided not to take part in an international naval review this week in South Korea after Seoul requested that Japanese vessels not fly the flag.

Some observers are concerned that renewed tensions between Japan and South Korea could impact the security of the region. "If our differences are aired in public, North Korea could take advantage of it," a Japanese government source said.