The EU took notice. In October, a formal agreement to launch the operation was signed by the two countries and the EU.
The mission's inauguration ceremony in Odesa today was attended by EU High Representative for the Foreign and Security Policy Javier Solana, European Commissioner for External Affairs and Neighborhood Policy Bettina Ferrero-Waldner, Ukrainian Foreign Minister Borys Tarasyuk, and Moldovan Foreign Minister Andrei Stratan.
The operation reportedly consists of some 70 border policemen and customs officers from 16 EU countries and 50 local staffers. It has a budget of 8 million euros ($9.4 million) and a two-year mandate, which can be extended.
Apart from its core headquarters in Odesa, it will have five field offices, from which it will be able to dispatch mobile teams to monitor the border.
The monitors are authorized to make unannounced inspections at any location on the Ukrainian-Moldovan frontier. However, they will not operate on Transdniestrian territory.
It is Transdniestria that seems to be the problem.
After a short conflict in 1992 with Moldovan forces, Transdniestrian separatists broke away. A ceasefire has held ever since, but the Council of Europe recognizes Transdniester as a "frozen conflict."
Both Ukraine and Moldova suspect that the separatist regime of Igor Smirnov in Transdniester may be involved in arms and drug smuggling through the porous border with Ukraine.
Oleh Dolzhenkov, an official from the Odesa City Council, shared such concerns with RFE/RL's Ukrainian Service.
"We know that the city of Odesa was drowning for a long time in illegal weapons, drugs, etc., which went through unmonitored sections of the Moldovan-Ukrainian border," Dolzhenkov said. "We know that some time ago a number of resonant crimes were perpetrated by organized crime groups operating from the territory of the unrecognized Moldovan Transdniestrian Republic, just because there has so far been no efficient system of monitoring of the movement of people and goods through this stretch of the border."
However, hard evidence to support such suspicions has not yet been produced. A team of EU experts who toured Moldova and Ukraine in August could not confirm the allegations that Tiraspol smuggles drugs and weapons to Ukraine.
There are also suspicions that some people on both sides of the border may be involved in transit-related fraud.
A possible deception scheme could look like this: Shipments of goods arriving by sea in Odesa are declared as Tiraspol bound and not taxed by Ukraine. Subsequently, authorities in Tiraspol confirm receipt, but the goods are rerouted to Ukraine.
In a broader perspective, the start of the new border operation can be seen as the EU's contribution to the resolution of the Transdniester conflict. Enforcing tighter controls could go some way in eroding the economic base of the separatist regime.
Earlier this year, Ukrainian President Viktor Yushchenko proposed a solution to the Transdniester conflict. Under his plan, the divided country would reintegrate under the Moldovan constitutional system and Transdniester would be granted a "special status." The plan also called for holding democratic elections to the Transdniestrian legislature under international monitoring.
However, the Moscow-supported regime in Tiraspol ignored Yushchenko's initiative and decided to hold legislative elections in December under its own legislation, thus excluding the possibility that they can be recognized by the international community.