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Based on information from L'Album 1990, and the illustration in correction 26, there are flags for the President, Chief of Staff, Chief of the Navy and there exists a war pennant.

The flag of the President of the Republic is an (approximately) square flag based on the design of the Togolese national flag but having the square canton covering a larger area than normal. In the canton the star from the national flag is replaced by a golden laurel wreath with a smaller white star in its base and between the branches are the initials GE in gold. These stand for Gnassingbé Eyadéma, the President of Togo who took the power in 1967 when using the name �tienne Eyadema [the accents are uncertain and are written differently in several sources I consulted]. Eyadema changed his name to Gnassingbé on 08 May 1974 (according to http://www.geocities.com/Athens/1058/rulers.html). The font, size and position of the initials is my interpretation ("reconstruction" if you will) since the image in L'Album does not contain any initials.

Depending on when this flag was adopted, it may be that EE might also have been used (but probably without accents. It may even be possible that former presidents had versions of their own following the French tradition. In that case here is the list from the source mentioned above:

27 Apr 1960 - 13 Jan 1963	Sylvanus Olympio (b. 1902 - d. 1963) (acting to 12 Apr 1961)
13 Jan 1963 - 15 Jan 1963	Emmanuel Bodjollé (b. 1928) (chairman Insurrection Committee)
16 Jan 1963 - 13 Jan 1967	Nicolas Grunitzky (b. 1913 - d. 1969) (acting to 5 May 1963)
14 Jan 1967 - 14 Apr 1967	Kléber Dadjo (b. 1914) (chairman National Reconciliation Committee)
14 Apr 1967 - 05 Feb 2005	Étienne Eyadema (from 8 May 1974, Gnassingbe Eyadema) (b. 1937)

Željko Heimer, 21 May 2000

Gnassingbe Eyadema ruled Togo under a one-party system and died of a heart attack on 05 February 2005. In terms of the Togolese Constitution, the President of the Parliament, Fambar� Ouattara Natchaba should have succeeded Eyadema as President pending the outcome of a Presidential election to be called within 60 days. However, Natchaba was out of the country at the time of Eyadema's death and the armed forces (Forces Arm�es Togolaises) closed the country's borders and refused to allow Natchaba to return to the country. With an engineered political vacuum, parliament voted to remove the clause requiring a Presidential election to be held within 60 days and declared Eyadema's son, Faure Gnassingb�, would "inherit" the presidency and hold office for the remainder of his father's term. Faure was sworn in as President on 07 February 2005, despite international criticism.

The African Union described the takeover as a coup d'etat and there was considerable opposition within the country, particularly in the south were there were reports of several deaths following civilian uprisings. In response, Faure Gnassingb� agreed to hold elections. On 24 April 2005, Gnassingb� was elected President of Togo after receiving over 60% of the vote according to official results and was sworn in as President on 03 May 2005. He was re-elected again in March 2010.
Bruce Berry, 08 June 2013

The flag of the Chief of General Staff of the Armed Forces (Chef de l'État-Major des Forces Armées) follows the same design as the flag of the President of Togo but with different detail contained in the red canton. Here a golden emblem consisting of two rifles in saltire, an anchor palewise and an emblem standing symbolically for wings, with over all a white five-pointed star.
Željko Heimer, 21 May 2000

The flag of the Commander in Chief of the Navy (Commandant de la Marine) is of the same design as the previous flags. In this instance the emblem in the red canton consists of two golden anchors in saltire and a white star superimposed in the middle of the canton. This star seems to be notably smaller than the one in the national flag (being about the same height as one stripe).
Željko Heimer, 21 May 2000

The Togolese war pennant (flamme de guerre) is a long triangular pennant of green over yellow with red panel at hoist.

The ratio of the pennant is given as 1:7~ in Correction 26 and 1:6.6~ in the original issue of L'Album 1990. The red field is given as less the 1/10 of the fly in the original L'Album 1990, and is not quoted in correction 26. The image in correction 26 shows a pennant of ratio about 1:11 (my estimate), with red field being of the same width as the hoist (but that would agree with "less the 1/10").
Željko Heimer, 21 May 2000

Togo - Government and Military Flags

Presidential Standard

Chief of General Staff of the Armed Forces

Commander in Chief of the Navy

War Pennant

Naval Ensign ?