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A subset $\mathcal{F}$ of a finite transitive group $G\leq \operatorname{Sym}(Ω)$ is \emph{intersecting} if any two elements of $\mathcal{F}$ agree on an element of $Ω$. The \emph{intersection density} of $G$ is the number $$ρ(G) = \max\left\{ \mathcal{|F|}/|G_ω| \mid \mathcal{F}\subset G \mbox{ is intersecting} \right\},$$ where $ω\inΩ$ and $G_ω$ is the stabilizer of $ω$ in $G$. It is known that if $G\leq \operatorname{Sym}(Ω)$ is an imprimitive group of degree a product of two odd primes $p>q$ admitting a block of size $p$ or two complete block systems, whose blocks are of size $q$, then $ρ(G) = 1$. In this paper, we analyse the intersection density of imprimitive groups of degree $pq$ with a unique block system with blocks of size $q$ based on the kernel of the induced action on blocks. For those whose kernels are non-trivial, it is proved that the intersection density is larger than $1$ whenever there exists a cyclic code $C$ with parameters $[p,k]_q$ such that any codeword of $C$ has weight at most $p-1$, and under some additional conditions on the cyclic code, it is a proper rational number. For those that are quasiprimitive, we reduce the cases to almost simple groups containing $\operatorname{Alt}(5)$ or a projective special linear group. We give some examples where the latter has intersection density equal to $1$, under some restrictions on $p$ and $q$.