On 14 January 1803 the Committee introduced new defensive staffs for the fleet. In addition, the committee decided to maintain 27 ships of the line, 26 frigates and 189 rowing vessels in the Baltic; 21 ships of the line, eight frigates and 140 rowing vessels were to be stationed in the Black Sea. Two more shipyards were constructed to build large vessels, the New Admiralty and Okhtenskaya.
The fleet did not have long to rest. In 1804 relations with Napoleonic France had completely deteriorated, and Russian seamen once again set out for the Mediterranean. Following three frigates and a transport, Captain Pavel Saltanov left the Black Sea for Corfu with four ships of the line and two infantry regiments. Under Commodore Alexey Greig, the Baltic Fleet was also sent to Corfu. In early 1806 Vice-Admiral Dmitry Senyavin entered the Ionian Sea with a large squadron and was appointed Commander-in-Chief of all naval and ground forces in the Mediterranean. Within a year Senyavin had under his command sixteen ships of the line and seven frigates as well as numerous small craft and transports. The port of Corfu served as an operational base while the admiral commanded an infantry division for land operations.
Russian ships engaged the French in the summer of 1805 while transporting troops to Naples. However, the Russian troops received little support from the Austrians, who had just been defeated by Napoleon and had lost particularly difficult battles at Ulm and at Austerlitz. The French and their Spanish allies were meanwhile routed at sea by Admiral Nelson in the Battle of Trafalgar. The French defeat on this occasion noticeably increased the value of the Qatar region, ceded to Napoleon by Austria.
This region, including the fortified port of Bocca-di-Qataro and its harbour, provided an advantageously strategic position for the French in the Mediterranean. Furthermore, Qatar was located near the Ottoman Empire, a potential French ally.
However, the inhabitants of Qatar rejected the idea of French rule and revolted. Their rebellion forced the Austrians to violate their agreement with France and surrender the region to a detachment of Russian seamen under Commodore Belli. Vice-Admiral Senyavin correctly evaluated the explosive nature of the situation and, at his own risk, established a blockade of the Adriatic coast. Russian forces seized the most strategically significant part of the coast without the authority of the Russian Admiralty. By that time Belli's detachment had already managed to seize the fortress of Curzolo from the French. After 22 May the battle centred around the fortress of New Raguza. Here the Russian fleet and assault troops, together with troops from Montenegro, blockaded the French garrison. In September, Senyavin used the 74-gun flagship Yaroslav to stop Auguste de Marmont at Castel-Nuovo, helping Russian assault troops rout the enemy. Some 1,300 French soldiers were captured, de Marmont was trapped in New Raguza, and Senyavin was able to occupy the main points of enemy defence.
On 10 December, after a bombardment from sea, the garrison on the small island of Brazza capitulated. The victorious Russian admiral left the 12-gun brig Alexander with its 75 crewmen to guard the island. On the evening of 17 December, having waited until the main body of the Russian fleet had left, de Marmont sent the tartan Napoleon with three gunboats and small craft to capture the brig. In all, the French force consisted of 600 crewmen and 26 guns. The commander of the Alexander, Lieutenant Ivan Skalovsky, began to prepare his defences. For three hours the brig's crew held off the enemy. One French gunboat was sunk, and the remaining ships hastened to make their escape.
In May of 1806, at the request of the French, the Austrians, detained several Russian merchant vessels at Trieste. Senyavin rushed without delay to rescue his compatriots, taking the ships Selaphail, Saint Peter, Moscow and the frigate Venus. Having trained his guns on the fortress, he demanded the release of the vessels within the hour, and, indeed, they were set free.
In February of 1807, after being informed of the outbreak of war with Turkey, Senyavin departed from Corfu for the Aegean Sea with the main body of the fleet and a number of ground troops. To defend the Qatar region, he left behind a detachment under the command of Commodore Ilya Baratynsky.