Yes, and no.
When making a melee attack against a target that isn't adjacent to you (such as with a reach weapon), use the rules for determining cover from ranged attacks.
This means that if you are attacking an opponent on the other side of a low wall, another creature, or anything that would normally be treated as cover if you were shooting/throwing a weapon at said opponent. However if there is nothing between you and the target's square that would generate cover then there is no penalty. You can flank with reach weapons without penalty.
To determine whether your target has cover from your ranged attack, choose a corner of your square. If any line from this corner to any corner of the target's square passes through a square or border that blocks line of effect or provides cover, or through a square occupied by a creature, the target has cover
In addition, the only penalty for using a reach weapon into melee(due to it being treated as a 'Ranged' attack) is that of the cover penalty. There is no need for Precise shot.